data_PQN
#
_chem_comp.id PQN
_chem_comp.name PHYLLOQUINONE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C31 H46 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "VITAMIN K1; 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2020-06-17
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 450.696
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PQN
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1JB0
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
PQN C1 C1 C 0 1 N N N N N N 91.831 123.841 66.026 1.378 -1.417 -6.211 C1 PQN 1
PQN O1 O1 O 0 1 N N N N N N 92.207 123.083 67.162 1.818 -2.451 -6.673 O1 PQN 2
PQN C2 C2 C 0 1 N N N N N N 90.583 124.552 66.031 -0.078 -1.230 -6.067 C2 PQN 3
PQN C2M C2M C 0 1 N N N N N N 89.799 124.498 67.141 -1.013 -2.331 -6.497 C2M PQN 4
PQN C3 C3 C 0 1 N N N N N N 90.192 125.330 64.854 -0.580 -0.096 -5.561 C3 PQN 5
PQN C4 C4 C 0 1 N N N N N N 91.058 125.383 63.720 0.307 1.002 -5.137 C4 PQN 6
PQN O4 O4 O 0 1 N N N N N N 90.655 126.110 62.564 -0.163 2.026 -4.684 O4 PQN 7
PQN C5 C5 C 0 1 Y N N N N N 92.312 124.686 63.729 1.773 0.850 -5.259 C5 PQN 8
PQN C6 C6 C 0 1 Y N N N N N 93.192 124.746 62.587 2.631 1.868 -4.861 C6 PQN 9
PQN C7 C7 C 0 1 Y N N N N N 94.435 124.042 62.603 4.001 1.703 -4.992 C7 PQN 10
PQN C8 C8 C 0 1 Y N N N N N 94.811 123.270 63.753 4.520 0.534 -5.515 C8 PQN 11
PQN C9 C9 C 0 1 Y N N N N N 93.945 123.202 64.891 3.676 -0.490 -5.916 C9 PQN 12
PQN C10 C10 C 0 1 Y N N N N N 92.697 123.903 64.894 2.300 -0.340 -5.791 C10 PQN 13
PQN C11 C11 C 0 1 N N N N N N 88.859 126.120 64.803 -2.073 0.060 -5.429 C11 PQN 14
PQN C12 C12 C 0 1 N N N N N N 89.036 127.439 65.582 -2.514 -0.444 -4.079 C12 PQN 15
PQN C13 C13 C 0 1 N N N N N N 88.609 128.669 64.791 -3.210 0.330 -3.285 C13 PQN 16
PQN C14 C14 C 0 1 N N N N N N 88.085 128.672 63.335 -3.678 1.679 -3.768 C14 PQN 17
PQN C15 C15 C 0 1 N N N N N N 88.848 129.901 65.726 -3.544 -0.126 -1.889 C15 PQN 18
PQN C16 C16 C 0 1 N N N N N N 88.308 131.059 65.292 -2.437 0.315 -0.929 C16 PQN 19
PQN C17 C17 C 0 1 N N N N N N 86.998 131.304 66.044 -2.776 -0.148 0.488 C17 PQN 20
PQN C18 C18 C 0 1 N N R N N N 86.780 132.813 66.324 -1.669 0.293 1.447 C18 PQN 21
PQN C19 C19 C 0 1 N N N N N N 86.096 132.935 67.678 -0.339 -0.325 1.012 C19 PQN 22
PQN C20 C20 C 0 1 N N N N N N 85.875 133.431 65.222 -2.008 -0.170 2.865 C20 PQN 23
PQN C21 C21 C 0 1 N N N N N N 85.549 134.908 65.550 -0.901 0.271 3.825 C21 PQN 24
PQN C22 C22 C 0 1 N N N N N N 84.211 135.311 64.866 -1.240 -0.192 5.243 C22 PQN 25
PQN C23 C23 C 0 1 N N R N N N 83.767 136.777 65.189 -0.133 0.249 6.202 C23 PQN 26
PQN C24 C24 C 0 1 N N N N N N 84.937 137.754 64.961 1.196 -0.369 5.767 C24 PQN 27
PQN C25 C25 C 0 1 N N N N N N 83.306 136.871 66.649 -0.472 -0.214 7.620 C25 PQN 28
PQN C26 C26 C 0 1 N N N N N N 82.565 138.190 66.890 0.634 0.227 8.580 C26 PQN 29
PQN C27 C27 C 0 1 N N N N N N 82.382 138.339 68.405 0.295 -0.236 9.998 C27 PQN 30
PQN C28 C28 C 0 1 N N N N N N 81.834 139.725 68.766 1.402 0.205 10.957 C28 PQN 31
PQN C29 C29 C 0 1 N N N N N N 81.586 139.739 70.280 1.063 -0.258 12.375 C29 PQN 32
PQN C30 C30 C 0 1 N N N N N N 82.851 140.822 68.429 2.732 -0.413 10.522 C30 PQN 33
PQN H2M1 1H2M H 0 0 N N N N N N 88.830 125.049 67.144 -0.434 -3.171 -6.881 H2M1 PQN 34
PQN H2M2 2H2M H 0 0 N N N N N N 89.604 123.429 67.392 -1.606 -2.658 -5.643 H2M2 PQN 35
PQN H2M3 3H2M H 0 0 N N N N N N 90.400 124.822 68.022 -1.677 -1.960 -7.278 H2M3 PQN 36
PQN H6 H6 H 0 1 N N N N N N 92.912 125.333 61.696 2.232 2.784 -4.452 H6 PQN 37
PQN H7 H7 H 0 1 N N N N N N 95.104 124.094 61.727 4.669 2.494 -4.683 H7 PQN 38
PQN H8 H8 H 0 1 N N N N N N 95.770 122.726 63.762 5.589 0.417 -5.611 H8 PQN 39
PQN H9 H9 H 0 1 N N N N N N 94.241 122.606 65.770 4.087 -1.402 -6.323 H9 PQN 40
PQN H111 1H11 H 0 0 N N N N N N 88.500 126.285 63.760 -2.569 -0.512 -6.212 H111 PQN 41
PQN H112 2H11 H 0 0 N N N N N N 87.993 125.520 65.170 -2.337 1.113 -5.527 H112 PQN 42
PQN H12 H12 H 0 1 N N N N N N 89.431 127.497 66.610 -2.256 -1.445 -3.767 H12 PQN 43
PQN H141 1H14 H 0 0 N N N N N N 87.772 129.572 62.756 -4.312 2.137 -3.010 H141 PQN 44
PQN H142 2H14 H 0 0 N N N N N N 88.857 128.153 62.720 -2.814 2.317 -3.954 H142 PQN 45
PQN H143 3H14 H 0 0 N N N N N N 87.223 127.964 63.307 -4.245 1.557 -4.691 H143 PQN 46
PQN H151 1H15 H 0 0 N N N N N N 88.494 129.674 66.759 -3.626 -1.213 -1.872 H151 PQN 47
PQN H152 2H15 H 0 0 N N N N N N 89.938 130.032 65.918 -4.491 0.314 -1.579 H152 PQN 48
PQN H161 1H16 H 0 0 N N N N N N 89.015 131.917 65.377 -2.355 1.402 -0.946 H161 PQN 49
PQN H162 2H16 H 0 0 N N N N N N 88.174 131.078 64.185 -1.490 -0.125 -1.239 H162 PQN 50
PQN H171 1H17 H 0 0 N N N N N N 86.128 130.858 65.506 -2.858 -1.235 0.504 H171 PQN 51
PQN H172 2H17 H 0 0 N N N N N N 86.946 130.702 66.981 -3.723 0.292 0.798 H172 PQN 52
PQN H18 H18 H 0 1 N N N N N N 87.754 133.355 66.324 -1.587 1.380 1.431 H18 PQN 53
PQN H191 1H19 H 0 0 N N N N N N 85.939 134.020 67.879 -0.422 -1.412 1.029 H191 PQN 54
PQN H192 2H19 H 0 0 N N N N N N 85.154 132.340 67.744 -0.098 0.005 0.002 H192 PQN 55
PQN H193 3H19 H 0 0 N N N N N N 86.653 132.418 68.493 0.448 -0.010 1.696 H193 PQN 56
PQN H201 1H20 H 0 0 N N N N N N 86.324 133.321 64.207 -2.090 -1.257 2.882 H201 PQN 57
PQN H202 2H20 H 0 0 N N N N N N 84.950 132.829 65.060 -2.955 0.270 3.175 H202 PQN 58
PQN H211 1H21 H 0 0 N N N N N N 85.535 135.102 66.647 -0.819 1.358 3.808 H211 PQN 59
PQN H212 2H21 H 0 0 N N N N N N 86.384 135.593 65.276 0.045 -0.169 3.515 H212 PQN 60
PQN H221 1H22 H 0 0 N N N N N N 84.264 135.147 63.764 -1.322 -1.279 5.259 H221 PQN 61
PQN H222 2H22 H 0 0 N N N N N N 83.402 134.587 65.121 -2.187 0.248 5.553 H222 PQN 62
PQN H23 H23 H 0 1 N N N N N N 82.925 137.050 64.511 -0.051 1.336 6.186 H23 PQN 63
PQN H241 1H24 H 0 0 N N N N N N 84.620 138.798 65.191 1.113 -1.456 5.783 H241 PQN 64
PQN H242 2H24 H 0 0 N N N N N N 85.844 137.457 65.537 1.437 -0.038 4.757 H242 PQN 65
PQN H243 3H24 H 0 0 N N N N N N 85.358 137.664 63.932 1.984 -0.054 6.450 H243 PQN 66
PQN H251 1H25 H 0 0 N N N N N N 82.693 135.989 66.948 -0.554 -1.301 7.637 H251 PQN 67
PQN H252 2H25 H 0 0 N N N N N N 84.152 136.733 67.361 -1.419 0.226 7.930 H252 PQN 68
PQN H261 1H26 H 0 0 N N N N N N 83.072 139.066 66.423 0.716 1.314 8.563 H261 PQN 69
PQN H262 2H26 H 0 0 N N N N N N 81.606 138.261 66.325 1.581 -0.213 8.269 H262 PQN 70
PQN H271 1H27 H 0 0 N N N N N N 81.744 137.525 68.822 0.213 -1.323 10.014 H271 PQN 71
PQN H272 2H27 H 0 0 N N N N N N 83.325 138.116 68.955 -0.651 0.204 10.308 H272 PQN 72
PQN H28 H28 H 0 1 N N N N N N 80.900 139.919 68.188 1.484 1.292 10.940 H28 PQN 73
PQN H291 1H29 H 0 0 N N N N N N 81.187 140.746 70.542 1.852 0.056 13.058 H291 PQN 74
PQN H292 2H29 H 0 0 N N N N N N 80.926 138.907 70.621 0.116 0.182 12.685 H292 PQN 75
PQN H293 3H29 H 0 0 N N N N N N 82.488 139.459 70.871 0.981 -1.345 12.392 H293 PQN 76
PQN H301 1H30 H 0 0 N N N N N N 82.452 141.829 68.691 2.649 -1.500 10.538 H301 PQN 77
PQN H302 2H30 H 0 0 N N N N N N 83.837 140.631 68.912 2.973 -0.082 9.511 H302 PQN 78
PQN H303 3H30 H 0 0 N N N N N N 83.172 140.771 67.362 3.520 -0.098 11.205 H303 PQN 79
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
PQN C1 O1 DOUB N N 1
PQN C1 C2 SING N N 2
PQN C1 C10 SING N N 3
PQN C2 C2M SING N N 4
PQN C2 C3 DOUB N N 5
PQN C2M H2M1 SING N N 6
PQN C2M H2M2 SING N N 7
PQN C2M H2M3 SING N N 8
PQN C3 C4 SING N N 9
PQN C3 C11 SING N N 10
PQN C4 O4 DOUB N N 11
PQN C4 C5 SING N N 12
PQN C5 C6 DOUB Y N 13
PQN C5 C10 SING Y N 14
PQN C6 C7 SING Y N 15
PQN C6 H6 SING N N 16
PQN C7 C8 DOUB Y N 17
PQN C7 H7 SING N N 18
PQN C8 C9 SING Y N 19
PQN C8 H8 SING N N 20
PQN C9 C10 DOUB Y N 21
PQN C9 H9 SING N N 22
PQN C11 C12 SING N N 23
PQN C11 H111 SING N N 24
PQN C11 H112 SING N N 25
PQN C12 C13 DOUB N E 26
PQN C12 H12 SING N N 27
PQN C13 C14 SING N N 28
PQN C13 C15 SING N N 29
PQN C14 H141 SING N N 30
PQN C14 H142 SING N N 31
PQN C14 H143 SING N N 32
PQN C15 C16 SING N N 33
PQN C15 H151 SING N N 34
PQN C15 H152 SING N N 35
PQN C16 C17 SING N N 36
PQN C16 H161 SING N N 37
PQN C16 H162 SING N N 38
PQN C17 C18 SING N N 39
PQN C17 H171 SING N N 40
PQN C17 H172 SING N N 41
PQN C18 C19 SING N N 42
PQN C18 C20 SING N N 43
PQN C18 H18 SING N N 44
PQN C19 H191 SING N N 45
PQN C19 H192 SING N N 46
PQN C19 H193 SING N N 47
PQN C20 C21 SING N N 48
PQN C20 H201 SING N N 49
PQN C20 H202 SING N N 50
PQN C21 C22 SING N N 51
PQN C21 H211 SING N N 52
PQN C21 H212 SING N N 53
PQN C22 C23 SING N N 54
PQN C22 H221 SING N N 55
PQN C22 H222 SING N N 56
PQN C23 C24 SING N N 57
PQN C23 C25 SING N N 58
PQN C23 H23 SING N N 59
PQN C24 H241 SING N N 60
PQN C24 H242 SING N N 61
PQN C24 H243 SING N N 62
PQN C25 C26 SING N N 63
PQN C25 H251 SING N N 64
PQN C25 H252 SING N N 65
PQN C26 C27 SING N N 66
PQN C26 H261 SING N N 67
PQN C26 H262 SING N N 68
PQN C27 C28 SING N N 69
PQN C27 H271 SING N N 70
PQN C27 H272 SING N N 71
PQN C28 C29 SING N N 72
PQN C28 C30 SING N N 73
PQN C28 H28 SING N N 74
PQN C29 H291 SING N N 75
PQN C29 H292 SING N N 76
PQN C29 H293 SING N N 77
PQN C30 H301 SING N N 78
PQN C30 H302 SING N N 79
PQN C30 H303 SING N N 80
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
PQN SMILES ACDLabs 10.04 O=C2c1c(cccc1)C(=O)C(=C2C)C\C=C(/C)CCCC(C)CCCC(C)CCCC(C)C
PQN SMILES_CANONICAL CACTVS 3.341 CC(C)CCC[C@@H](C)CCC[C@@H](C)CCCC(/C)=C/CC1=C(C)C(=O)c2ccccc2C1=O
PQN SMILES CACTVS 3.341 CC(C)CCC[CH](C)CCC[CH](C)CCCC(C)=CCC1=C(C)C(=O)c2ccccc2C1=O
PQN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC1=C(C(=O)c2ccccc2C1=O)C\C=C(/C)\CCC[C@H](C)CCC[C@H](C)CCCC(C)C
PQN SMILES "OpenEye OEToolkits" 1.5.0 CC1=C(C(=O)c2ccccc2C1=O)CC=C(C)CCCC(C)CCCC(C)CCCC(C)C
PQN InChI InChI 1.03 InChI=1S/C31H46O2/c1-22(2)12-9-13-23(3)14-10-15-24(4)16-11-17-25(5)20-21-27-26(6)30(32)28-18-7-8-19-29(28)31(27)33/h7-8,18-20,22-24H,9-17,21H2,1-6H3/b25-20+/t23-,24-/m1/s1
PQN InChIKey InChI 1.03 MBWXNTAXLNYFJB-NKFFZRIASA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
PQN "SYSTEMATIC NAME" ACDLabs 10.04 2-methyl-3-[(2E,7R,11R)-3,7,11,15-tetramethylhexadec-2-en-1-yl]naphthalene-1,4-dione
PQN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 2-methyl-3-[(E,7R,11R)-3,7,11,15-tetramethylhexadec-2-enyl]naphthalene-1,4-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PQN 'Create component' 1999-07-08 RCSB
PQN 'Modify descriptor' 2011-06-04 RCSB
PQN 'Modify synonyms' 2020-06-05 PDBE
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 PQN "VITAMIN K1" ? ?
2 PQN 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id PQN
_pdbe_chem_comp_drugbank_details.drugbank_id DB01022
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Phylloquinone
_pdbe_chem_comp_drugbank_details.description
'Vitamin K1, also called phylloquinone or phytonadione, is a fat soluble vitamin.[L33319,L33345] Phylloquinone is a cofactor of the enzyme γ-carboxylase, which modifies and activates precursors to coagulation factors II, VII, IX, and X.[A234264,A234195,A234259] It is indicated in the treatment of coagulation disorders due to faulty formation of coagulation factors II, VII, IX, and X caused by deficiency or interference in the activity of vitamin K.[L33319]  Phylloquinone has been synthesized since at least 1939,[A234384] and was approved by the FDA prior to 1955.[L33389]'
_pdbe_chem_comp_drugbank_details.cas_number 84-80-0
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Vitamin K is a cofactor of gamma-carboxylase.[A234264,A234195] Gamma carboxylase attaches carboxylic acid functional groups to glutamate, allowing precursors of factors II, VII, IX, and X to bind calcium ions.[A234259] Binding of calcium ions converts these clotting factors to their active form, which are then secreted from hepatocytes into the blood, restoring normal clotting function.[L33345]  Vitamin K may also carboxylate matrix proteins in chondrocytes, inhibiting calcification of joints, and may increase type II collagen.[A234304] The role of vitamin K in osteroarthritis,[A234304] bone density,[A234309] and vascular calcification[A234314] is currently under investigation.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
PQN Aquamephyton ChEMBL Tradename
PQN Konakion ChEMBL Tradename
PQN Mephyton ChEMBL Tradename
PQN Phylloquinone ChEMBL Tradename
PQN Phytomenadione ChEMBL Tradename
PQN Phytonadione ChEMBL Tradename
PQN Phytonadione ChEMBL 'United States Accepted Names'
PQN 'Vitamin K 1' ChEMBL Tradename
PQN 'Vitamin K1' ChEMBL Tradename
PQN 'VITAMIN K1' wwPDB ?
PQN 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE wwPDB ?
PQN 2-Methyl-3-(3,7,11,15-tetramethyl-2-hexadecenyl)-1,4-naphthalenedione DrugBank ?
PQN '2-Methyl-3-[(2E)-3,7,11,15-tetramethyl-2-hexadecenyl]naphthoquinone' DrugBank ?
PQN 2-Methyl-3-phytyl-1,4-naphthoquinone DrugBank ?
PQN 3-Phytylmenadione DrugBank ?
PQN alpha-Phylloquinone DrugBank ?
PQN Phyllochinonum DrugBank ?
PQN Phylloquinone DrugBank ?
PQN Phytomenadione DrugBank ?
PQN Phytomenadionum DrugBank ?
PQN Phytonadione DrugBank ?
PQN Phytonadionum DrugBank ?
PQN Phytylmenadione DrugBank ?
PQN trans-Phylloquinone DrugBank ?
PQN 'Vitamin K' DrugBank ?
PQN 'Vitamin K1' DrugBank ?
PQN 'α-phylloquinone' DrugBank ?
PQN Aqua-Mephyton DrugBank 'International brand'
PQN Konakion DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id PQN
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01022
_pdbe_chem_comp_drugbank_classification.parent 'Vitamin K compounds'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Prenol lipids'
_pdbe_chem_comp_drugbank_classification.superclass 'Lipids and lipid-like molecules'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as vitamin k compounds. These are quinone lipids containing a methylated naphthoquinone ring structure, and vary in the aliphatic side chain attached at the 3-position.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
PQN DB01022 'Vitamin K-dependent gamma-carboxylase' Humans P38435 yes 1
PQN DB01022 Osteocalcin Humans P02818 unknown 2
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
PQN C1 C 25.084 1.500 1
PQN O1 O 25.084 3.000 2
PQN C2 C 23.785 0.750 3
PQN C2M C 22.486 1.500 4
PQN C3 C 23.785 -0.750 5
PQN C4 C 25.084 -1.500 6
PQN O4 O 25.084 -3.000 7
PQN C5 C 26.383 -0.750 8
PQN C6 C 27.724 -1.552 9
PQN C7 C 29.083 -0.781 10
PQN C8 C 29.083 0.781 11
PQN C9 C 27.724 1.552 12
PQN C10 C 26.383 0.750 13
PQN C11 C 22.486 -1.500 14
PQN C12 C 21.187 -0.750 15
PQN C13 C 19.887 -1.500 16
PQN C14 C 19.887 -3.000 17
PQN C15 C 18.588 -0.750 18
PQN C16 C 17.290 -1.500 19
PQN C17 C 15.990 -0.750 20
PQN C18 C 14.691 -1.500 21
PQN C19 C 14.691 -3.000 22
PQN C20 C 13.392 -0.750 23
PQN C21 C 12.093 -1.500 24
PQN C22 C 10.794 -0.750 25
PQN C23 C 9.495 -1.500 26
PQN C24 C 9.495 -3.000 27
PQN C25 C 8.196 -0.750 28
PQN C26 C 6.897 -1.500 29
PQN C27 C 5.598 -0.750 30
PQN C28 C 4.299 -1.500 31
PQN C29 C 3.000 -0.750 32
PQN C30 C 4.299 -3.000 33
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
PQN C1 O1 DOUBLE NONE 1
PQN C1 C2 SINGLE NONE 2
PQN C1 C10 SINGLE NONE 3
PQN C2 C2M SINGLE NONE 4
PQN C2 C3 DOUBLE NONE 5
PQN C3 C4 SINGLE NONE 6
PQN C3 C11 SINGLE NONE 7
PQN C4 O4 DOUBLE NONE 8
PQN C4 C5 SINGLE NONE 9
PQN C5 C6 SINGLE NONE 10
PQN C5 C10 DOUBLE NONE 11
PQN C6 C7 DOUBLE NONE 12
PQN C7 C8 SINGLE NONE 13
PQN C8 C9 DOUBLE NONE 14
PQN C9 C10 SINGLE NONE 15
PQN C11 C12 SINGLE ENDUPRIGHT 16
PQN C12 C13 DOUBLE NONE 17
PQN C13 C14 SINGLE ENDDOWNRIGHT 18
PQN C13 C15 SINGLE ENDUPRIGHT 19
PQN C15 C16 SINGLE NONE 20
PQN C16 C17 SINGLE NONE 21
PQN C17 C18 SINGLE NONE 22
PQN C18 C19 SINGLE BEGINDASH 23
PQN C18 C20 SINGLE NONE 24
PQN C20 C21 SINGLE NONE 25
PQN C21 C22 SINGLE NONE 26
PQN C22 C23 SINGLE NONE 27
PQN C23 C24 SINGLE BEGINDASH 28
PQN C23 C25 SINGLE NONE 29
PQN C25 C26 SINGLE NONE 30
PQN C26 C27 SINGLE NONE 31
PQN C27 C28 SINGLE NONE 32
PQN C28 C29 SINGLE NONE 33
PQN C28 C30 SINGLE NONE 34
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
PQN MurckoScaffold S1 scaffold O=C1C=CC(=O)c2ccccc21 InChI=1S/C10H6O2/c11-9-5-6-10(12)8-4-2-1-3-7(8)9/h1-6H FRASJONUBLZVQX-UHFFFAOYSA-N
PQN phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
PQN C1 S1 1
PQN O1 S1 1
PQN C2 S1 1
PQN C3 S1 1
PQN C4 S1 1
PQN O4 S1 1
PQN C5 S1 1
PQN C6 S1 1
PQN C7 S1 1
PQN C8 S1 1
PQN C9 S1 1
PQN C10 S1 1
PQN C5 F1 1
PQN C6 F1 1
PQN C7 F1 1
PQN C8 F1 1
PQN C9 F1 1
PQN C10 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PQN
_pdbe_chem_comp_rdkit_properties.exactmw 450.350
_pdbe_chem_comp_rdkit_properties.amw 450.707
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 20
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 33
_pdbe_chem_comp_rdkit_properties.NumAtoms 79
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.613
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 267.122
_pdbe_chem_comp_rdkit_properties.tpsa 34.140
_pdbe_chem_comp_rdkit_properties.CrippenClogP 9.048
_pdbe_chem_comp_rdkit_properties.CrippenMR 140.364
_pdbe_chem_comp_rdkit_properties.chi0v 16.316
_pdbe_chem_comp_rdkit_properties.chi1v 8.408
_pdbe_chem_comp_rdkit_properties.chi2v 3.283
_pdbe_chem_comp_rdkit_properties.chi3v 3.283
_pdbe_chem_comp_rdkit_properties.chi4v 1.937
_pdbe_chem_comp_rdkit_properties.chi0n 62.316
_pdbe_chem_comp_rdkit_properties.chi1n 31.408
_pdbe_chem_comp_rdkit_properties.chi2n 3.283
_pdbe_chem_comp_rdkit_properties.chi3n 3.283
_pdbe_chem_comp_rdkit_properties.chi4n 1.937
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.960
_pdbe_chem_comp_rdkit_properties.kappa1 4.599
_pdbe_chem_comp_rdkit_properties.kappa2 13.676
_pdbe_chem_comp_rdkit_properties.kappa3 8.721
_pdbe_chem_comp_rdkit_properties.Phi 1.906
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
PQN UniChem ChEMBL CHEMBL1550
PQN UniChem DrugBank DB01022
PQN UniChem PDBe PQN
PQN UniChem ChEBI 18067
PQN UniChem ZINC ZINC000003831332
PQN UniChem fdasrs MLF3D1712D
PQN UniChem fdasrs S5Z3U87QHF
PQN UniChem HMDB HMDB0003555
PQN UniChem NMRShiftDB 60019460
PQN UniChem Recon phyQ
PQN UniChem DrugCentral 2843
PQN UniChem MetaboLights MTBLC18067
PQN UniChem BRENDA 1422
PQN UniChem BRENDA 245056
PQN UniChem BRENDA 3674
PQN UniChem BRENDA 6015
PQN UniChem BRENDA 6036
PQN UniChem Rhea 18067
PQN UniChem DailyMed PHYTONADIONE
PQN UniChem ClinicalTrials AQUAMEPHYTON
PQN UniChem ClinicalTrials KONAKION
PQN UniChem ClinicalTrials MEPHYTON
PQN UniChem ClinicalTrials PHYLLOQUINONE
PQN UniChem ClinicalTrials PHYTOMENADIONE
PQN UniChem ClinicalTrials PHYTONADIONE
PQN UniChem ClinicalTrials VETA-K1
PQN UniChem ClinicalTrials 'VITAMIN K'
PQN UniChem ClinicalTrials 'VITAMIN K1'
PQN UniChem rxnorm MEPHYTON
PQN UniChem rxnorm 'VITAMIN K1'
PQN UniChem MedChemExpress HY-N0684
PQN UniChem 'Probes And Drugs' PD000381
PQN UniChem SwissLipids SLM:000390033
PQN UniChem SureChEMBL SCHEMBL3882
PQN UniChem 'PubChem TPHARMA' 14784161
PQN UniChem 'PubChem TPHARMA' 16114315
PQN UniChem PubChem 5284607
PQN UniChem Nikkaji J3.883K
PQN UniChem 'EPA CompTox Dashboard' DTXSID8023472
PQN UniChem LipidMaps LMPR02030028
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
PQN C1 8.164 -0.889 0.353 ETKDGv3 1
PQN O1 8.999 -1.435 1.124 ETKDGv3 2
PQN C2 7.140 0.043 0.900 ETKDGv3 3
PQN C2M 7.105 0.297 2.391 ETKDGv3 4
PQN C3 6.289 0.676 0.052 ETKDGv3 5
PQN C4 6.329 0.357 -1.401 ETKDGv3 6
PQN O4 5.495 0.886 -2.185 ETKDGv3 7
PQN C5 7.336 -0.586 -1.933 ETKDGv3 8
PQN C6 7.390 -0.887 -3.388 ETKDGv3 9
PQN C7 8.303 -1.739 -3.868 ETKDGv3 10
PQN C8 9.263 -2.386 -2.954 ETKDGv3 11
PQN C9 9.223 -2.123 -1.643 ETKDGv3 12
PQN C10 8.213 -1.179 -1.097 ETKDGv3 13
PQN C11 5.238 1.652 0.548 ETKDGv3 14
PQN C12 3.971 0.926 0.930 ETKDGv3 15
PQN C13 2.875 1.553 1.407 ETKDGv3 16
PQN C14 2.845 3.051 1.597 ETKDGv3 17
PQN C15 1.650 0.737 1.759 ETKDGv3 18
PQN C16 0.879 0.342 0.491 ETKDGv3 19
PQN C17 -0.314 -0.587 0.780 ETKDGv3 20
PQN C18 -1.421 0.010 1.690 ETKDGv3 21
PQN C19 -2.570 -0.997 1.845 ETKDGv3 22
PQN C20 -1.939 1.409 1.258 ETKDGv3 23
PQN C21 -2.600 1.472 -0.139 ETKDGv3 24
PQN C22 -4.138 1.458 -0.058 ETKDGv3 25
PQN C23 -4.813 1.194 -1.427 ETKDGv3 26
PQN C24 -4.484 2.310 -2.434 ETKDGv3 27
PQN C25 -6.353 1.066 -1.300 ETKDGv3 28
PQN C26 -6.862 -0.044 -0.357 ETKDGv3 29
PQN C27 -6.335 -1.444 -0.729 ETKDGv3 30
PQN C28 -6.924 -2.598 0.116 ETKDGv3 31
PQN C29 -8.436 -2.765 -0.084 ETKDGv3 32
PQN C30 -6.578 -2.467 1.606 ETKDGv3 33
PQN H2M1 7.523 1.302 2.609 ETKDGv3 34
PQN H2M2 6.064 0.236 2.773 ETKDGv3 35
PQN H2M3 7.696 -0.454 2.953 ETKDGv3 36
PQN H6 6.692 -0.420 -4.071 ETKDGv3 37
PQN H7 8.340 -1.956 -4.927 ETKDGv3 38
PQN H8 9.999 -3.075 -3.348 ETKDGv3 39
PQN H9 9.934 -2.606 -0.985 ETKDGv3 40
PQN H111 5.009 2.393 -0.247 ETKDGv3 41
PQN H112 5.617 2.237 1.412 ETKDGv3 42
PQN H12 3.945 -0.156 0.815 ETKDGv3 43
PQN H141 3.616 3.355 2.336 ETKDGv3 44
PQN H142 3.037 3.561 0.630 ETKDGv3 45
PQN H143 1.856 3.393 1.968 ETKDGv3 46
PQN H151 0.991 1.324 2.431 ETKDGv3 47
PQN H152 1.957 -0.174 2.319 ETKDGv3 48
PQN H161 1.566 -0.201 -0.194 ETKDGv3 49
PQN H162 0.541 1.250 -0.051 ETKDGv3 50
PQN H171 0.076 -1.512 1.258 ETKDGv3 51
PQN H172 -0.749 -0.905 -0.191 ETKDGv3 52
PQN H18 -0.986 0.132 2.706 ETKDGv3 53
PQN H191 -2.193 -1.936 2.305 ETKDGv3 54
PQN H192 -3.014 -1.248 0.859 ETKDGv3 55
PQN H193 -3.360 -0.586 2.509 ETKDGv3 56
PQN H201 -1.094 2.128 1.286 ETKDGv3 57
PQN H202 -2.646 1.785 2.031 ETKDGv3 58
PQN H211 -2.283 2.420 -0.624 ETKDGv3 59
PQN H212 -2.249 0.644 -0.786 ETKDGv3 60
PQN H221 -4.435 0.663 0.650 ETKDGv3 61
PQN H222 -4.495 2.426 0.359 ETKDGv3 62
PQN H23 -4.412 0.248 -1.851 ETKDGv3 63
PQN H241 -3.401 2.316 -2.675 ETKDGv3 64
PQN H242 -4.772 3.303 -2.027 ETKDGv3 65
PQN H243 -5.029 2.144 -3.387 ETKDGv3 66
PQN H251 -6.770 2.035 -0.946 ETKDGv3 67
PQN H252 -6.783 0.878 -2.308 ETKDGv3 68
PQN H261 -7.970 -0.040 -0.423 ETKDGv3 69
PQN H262 -6.606 0.206 0.692 ETKDGv3 70
PQN H271 -5.232 -1.468 -0.605 ETKDGv3 71
PQN H272 -6.549 -1.640 -1.803 ETKDGv3 72
PQN H28 -6.444 -3.534 -0.247 ETKDGv3 73
PQN H291 -8.774 -3.716 0.380 ETKDGv3 74
PQN H292 -8.681 -2.804 -1.167 ETKDGv3 75
PQN H293 -9.000 -1.933 0.387 ETKDGv3 76
PQN H301 -7.121 -1.617 2.070 ETKDGv3 77
PQN H302 -5.486 -2.314 1.737 ETKDGv3 78
PQN H303 -6.864 -3.396 2.143 ETKDGv3 79
#