data_UDP
#
_chem_comp.id UDP
_chem_comp.name "URIDINE-5'-DIPHOSPHATE"
_chem_comp.type 'RNA LINKING'
_chem_comp.pdbx_type ATOMN
_chem_comp.formula 'C9 H14 N2 O12 P2'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2024-09-27
_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 404.161
_chem_comp.one_letter_code N
_chem_comp.three_letter_code UDP
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1NAH
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
UDP N1 N1 N 0 1 N N N N N N 15.861 15.192 39.665 -3.586 0.410 0.193 N1 UDP 1
UDP C2 C2 C 0 1 N N N N N N 15.566 16.502 40.157 -4.585 0.798 1.007 C2 UDP 2
UDP N3 N3 N 0 1 N N N N N N 16.683 17.291 40.382 -5.335 1.877 0.717 N3 UDP 3
UDP C4 C4 C 0 1 N N N N N N 18.033 16.891 40.187 -5.094 2.591 -0.401 C4 UDP 4
UDP C5 C5 C 0 1 N N N N N N 18.234 15.529 39.704 -4.045 2.195 -1.266 C5 UDP 5
UDP C6 C6 C 0 1 N N N N N N 17.189 14.755 39.468 -3.309 1.107 -0.951 C6 UDP 6
UDP O2 O2 O 0 1 N N N N N N 14.442 16.927 40.336 -4.815 0.163 2.019 O2 UDP 7
UDP O4 O4 O 0 1 N N N N N N 18.907 17.729 40.403 -5.771 3.568 -0.665 O4 UDP 8
UDP "C1'" "C1'" C 0 1 N N R N N N 14.733 14.256 39.447 -2.784 -0.766 0.539 "C1'" UDP 9
UDP "C2'" "C2'" C 0 1 N N R N N N 14.571 13.772 38.009 -2.990 -1.893 -0.505 "C2'" UDP 10
UDP "O2'" "O2'" O 0 1 N N N N N N 13.698 14.717 37.300 -4.127 -2.694 -0.174 "O2'" UDP 11
UDP "C3'" "C3'" C 0 1 N N S N N N 13.871 12.378 38.197 -1.681 -2.708 -0.366 "C3'" UDP 12
UDP "C4'" "C4'" C 0 1 N N R N N N 14.520 11.865 39.442 -0.691 -1.722 0.283 "C4'" UDP 13
UDP "O4'" "O4'" O 0 1 N N N N N N 14.969 13.076 40.161 -1.375 -0.468 0.438 "O4'" UDP 14
UDP "O3'" "O3'" O 0 1 N N N N N N 12.489 12.489 38.456 -1.885 -3.842 0.479 "O3'" UDP 15
UDP "C5'" "C5'" C 0 1 N N N N N N 15.675 10.964 39.264 0.530 -1.540 -0.621 "C5'" UDP 16
UDP "O5'" "O5'" O 0 1 N N N N N N 16.615 11.736 38.492 1.494 -0.718 0.040 "O5'" UDP 17
UDP PA PA P 0 1 N N N N N N 18.056 11.086 38.175 2.907 -0.318 -0.621 PA UDP 18
UDP O1A O1A O 0 1 N N N N N N 18.751 11.990 37.180 3.630 -1.546 -1.019 O1A UDP 19
UDP O2A O2A O 0 1 N N N N N N 18.899 10.824 39.383 2.651 0.599 -1.920 O2A UDP 20
UDP O3A O3A O 0 1 N N N N N N 17.921 9.607 37.471 3.787 0.501 0.449 O3A UDP 21
UDP PB PB P 0 1 N N N N N N 16.971 9.089 36.332 5.343 0.907 0.541 PB UDP 22
UDP O1B O1B O 0 1 N N N N N N 17.723 7.785 35.830 6.176 -0.227 0.081 O1B UDP 23
UDP O2B O2B O 0 1 N Y N N N N 16.843 10.179 35.297 5.619 2.189 -0.393 O2B UDP 24
UDP O3B O3B O 0 1 N N N N N N 15.643 8.680 36.921 5.716 1.263 2.066 O3B UDP 25
UDP HN3 HN3 H 0 1 N N N N N N 16.526 18.222 40.710 -6.052 2.143 1.314 HN3 UDP 26
UDP H5 H5 H 0 1 N N N N N N 19.234 15.154 39.540 -3.837 2.754 -2.166 H5 UDP 27
UDP H6 H6 H 0 1 N N N N N N 17.357 13.750 39.111 -2.506 0.790 -1.599 H6 UDP 28
UDP "H1'" "H1'" H 0 1 N N N N N N 13.844 14.827 39.755 -3.034 -1.119 1.539 "H1'" UDP 29
UDP "H2'" "H2'" H 0 1 N N N N N N 15.504 13.699 37.430 -3.087 -1.480 -1.510 "H2'" UDP 30
UDP "HO2'" "HO2'" H 0 0 N N N N N N 13.585 14.431 36.401 -4.297 -3.412 -0.798 "HO2'" UDP 31
UDP "H3'" "H3'" H 0 1 N N N N N N 13.971 11.753 37.297 -1.321 -3.021 -1.346 "H3'" UDP 32
UDP "H4'" "H4'" H 0 1 N N N N N N 13.783 11.242 39.970 -0.380 -2.098 1.258 "H4'" UDP 33
UDP "HO3'" "HO3'" H 0 0 N N N N N N 12.115 11.622 38.561 -2.544 -4.467 0.146 "HO3'" UDP 34
UDP "H5'1" "H5'1" H 0 0 N N N N N N 16.103 10.670 40.234 0.970 -2.514 -0.837 "H5'1" UDP 35
UDP "H5'2" "H5'2" H 0 0 N N N N N N 15.385 10.045 38.734 0.225 -1.064 -1.553 "H5'2" UDP 36
UDP HOA2 HOA2 H 0 0 N N N N N N 19.727 11.282 39.297 2.179 1.422 -1.733 HOA2 UDP 37
UDP HOB2 HOB2 H 0 0 N N N N N N 17.248 9.895 34.486 5.105 2.971 -0.148 HOB2 UDP 38
UDP HOB3 HOB3 H 0 0 N N N N N N 15.547 7.737 36.863 6.640 1.517 2.196 HOB3 UDP 39
#
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
UDP N1 C2 SING N N 1
UDP N1 C6 SING N N 2
UDP N1 "C1'" SING N N 3
UDP C2 N3 SING N N 4
UDP C2 O2 DOUB N N 5
UDP N3 C4 SING N N 6
UDP N3 HN3 SING N N 7
UDP C4 C5 SING N N 8
UDP C4 O4 DOUB N N 9
UDP C5 C6 DOUB N N 10
UDP C5 H5 SING N N 11
UDP C6 H6 SING N N 12
UDP "C1'" "C2'" SING N N 13
UDP "C1'" "O4'" SING N N 14
UDP "C1'" "H1'" SING N N 15
UDP "C2'" "O2'" SING N N 16
UDP "C2'" "C3'" SING N N 17
UDP "C2'" "H2'" SING N N 18
UDP "O2'" "HO2'" SING N N 19
UDP "C3'" "C4'" SING N N 20
UDP "C3'" "O3'" SING N N 21
UDP "C3'" "H3'" SING N N 22
UDP "C4'" "O4'" SING N N 23
UDP "C4'" "C5'" SING N N 24
UDP "C4'" "H4'" SING N N 25
UDP "O3'" "HO3'" SING N N 26
UDP "C5'" "O5'" SING N N 27
UDP "C5'" "H5'1" SING N N 28
UDP "C5'" "H5'2" SING N N 29
UDP "O5'" PA SING N N 30
UDP PA O1A DOUB N N 31
UDP PA O2A SING N N 32
UDP PA O3A SING N N 33
UDP O2A HOA2 SING N N 34
UDP O3A PB SING N N 35
UDP PB O1B DOUB N N 36
UDP PB O2B SING N N 37
UDP PB O3B SING N N 38
UDP O2B HOB2 SING N N 39
UDP O3B HOB3 SING N N 40
#
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
UDP SMILES ACDLabs 12.01 'O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O'
UDP SMILES_CANONICAL CACTVS 3.370 'O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O'
UDP SMILES CACTVS 3.370 'O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O'
UDP SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.0 'C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O'
UDP SMILES 'OpenEye OEToolkits' 1.7.0 'C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O'
UDP InChI InChI 1.03 'InChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1'
UDP InChIKey InChI 1.03 XCCTYIAWTASOJW-XVFCMESISA-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
UDP 'SYSTEMATIC NAME' ACDLabs 12.01
;uridine 5'-(trihydrogen diphosphate)
;
UDP 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.0 '[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphono hydrogen phosphate'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
UDP 'Create component' 1999-07-08 RCSB
UDP 'Modify descriptor' 2011-06-04 RCSB
UDP 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id UDP
_pdbx_chem_comp_pcm.modified_residue_id SRZ
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom O3B
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom CZ
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id UDP
_pdbe_chem_comp_drugbank_details.drugbank_id DB03435
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name "Uridine-5'-Diphosphate"
_pdbe_chem_comp_drugbank_details.description
'A uracil nucleotide containing a pyrophosphate group esterified to C5 of the sugar moiety. [PubChem]'
_pdbe_chem_comp_drugbank_details.cas_number 58-98-0
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id UDP
_pdbe_chem_comp_synonyms.name "Uridine-5'-Diphosphate"
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id UDP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03435
_pdbe_chem_comp_drugbank_classification.parent 'Pyrimidine ribonucleoside diphosphates'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Pyrimidine nucleotides'
_pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as pyrimidine ribonucleoside diphosphates. These are pyrimidine ribonucleotides with diphosphate group  linked to the ribose moiety.'
#
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
UDP DB03435 'UDP-N-acetylglucosamine 2-epimerase' 'Escherichia coli (strain K12)' P27828 unknown 1
UDP DB03435 'Histo-blood group ABO system transferase' Humans P16442 unknown 2
UDP DB03435 'Galactose-1-phosphate uridylyltransferase' 'Escherichia coli (strain K12)' P09148 unknown 3
UDP DB03435 'Pol polyprotein' FIV P16088 unknown 4
UDP DB03435 'Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1' Humans Q9P2W7 unknown 5
UDP DB03435 'Trehalose-6-phosphate synthase' 'Escherichia coli (strain K12)' P31677 unknown 6
UDP DB03435 'Exostosin-like 2' Humans Q9UBQ6 unknown 7
UDP DB03435 'Putative glycosyltransferase 6 domain-containing protein 1' Humans Q7Z4J2 unknown 8
UDP DB03435 'Spore coat polysaccharide biosynthesis protein SpsA' 'Bacillus subtilis (strain 168)' P39621 unknown 9
UDP DB03435 'UMP-CMP kinase' Humans P30085 unknown 10
UDP DB03435 'DNA beta-glucosyltransferase' 'Enterobacteria phage T4' P04547 unknown 11
UDP DB03435 'UDP-glucose 4-epimerase' 'Escherichia coli (strain K12)' P09147 unknown 12
UDP DB03435 'Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 3' Humans O94766 unknown 13
UDP DB03435 'UDP-glucose 4-epimerase' 'Trypanosoma brucei' Q8T8E9 unknown 14
UDP DB03435 Glycogenin-1 Humans P46976 unknown 15
UDP DB03435 'Uracil nucleotide/cysteinyl leukotriene receptor' Humans Q13304 unknown 16
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
UDP N1 N 6.331 2.337 1
UDP C2 C 7.630 3.087 2
UDP N3 N 7.630 4.587 3
UDP C4 C 6.331 5.337 4
UDP C5 C 5.032 4.587 5
UDP C6 C 5.032 3.087 6
UDP O2 O 8.929 2.337 7
UDP O4 O 6.331 6.837 8
UDP "C1'" C 6.331 0.837 9
UDP "C2'" C 5.118 -0.045 10
UDP "O2'" O 3.691 0.419 11
UDP "C3'" C 5.581 -1.471 12
UDP "C4'" C 7.081 -1.471 13
UDP "O4'" O 7.545 -0.045 14
UDP "O3'" O 4.699 -2.685 15
UDP "C5'" C 7.963 -2.685 16
UDP "O5'" O 9.455 -2.528 17
UDP PA P 10.336 -3.742 18
UDP O1A O 11.550 -2.860 19
UDP O2A O 9.123 -4.623 20
UDP O3A O 11.218 -4.955 21
UDP PB P 12.710 -4.798 22
UDP O1B O 14.202 -4.642 23
UDP O2B O 12.867 -6.290 24
UDP O3B O 12.553 -3.307 25
#
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
UDP N1 C2 SINGLE NONE 1
UDP N1 C6 SINGLE NONE 2
UDP "C1'" N1 SINGLE BEGINDASH 3
UDP C2 N3 SINGLE NONE 4
UDP C2 O2 DOUBLE NONE 5
UDP N3 C4 SINGLE NONE 6
UDP C4 C5 SINGLE NONE 7
UDP C4 O4 DOUBLE NONE 8
UDP C5 C6 DOUBLE NONE 9
UDP "C1'" "C2'" SINGLE NONE 10
UDP "C1'" "O4'" SINGLE NONE 11
UDP "C2'" "O2'" SINGLE BEGINWEDGE 12
UDP "C2'" "C3'" SINGLE NONE 13
UDP "C3'" "C4'" SINGLE NONE 14
UDP "C3'" "O3'" SINGLE BEGINWEDGE 15
UDP "C4'" "O4'" SINGLE NONE 16
UDP "C4'" "C5'" SINGLE BEGINDASH 17
UDP "C5'" "O5'" SINGLE NONE 18
UDP "O5'" PA SINGLE NONE 19
UDP PA O1A DOUBLE NONE 20
UDP PA O2A SINGLE BEGINWEDGE 21
UDP PA O3A SINGLE NONE 22
UDP O3A PB SINGLE NONE 23
UDP PB O1B DOUBLE NONE 24
UDP PB O2B SINGLE NONE 25
UDP PB O3B SINGLE NONE 26
#
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
UDP MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CCCO2)c(=O)[nH]1' InChI=1S/C8H10N2O3/c11-6-3-4-10(8(12)9-6)7-2-1-5-13-7/h3-4,7H,1-2,5H2,(H,9,11,12)/t7-/m1/s1 CWWIKVUHBBTKHC-SSDOTTSWSA-N
UDP phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
UDP pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
UDP ribose F3 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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
UDP N1 S1 1
UDP C2 S1 1
UDP N3 S1 1
UDP C4 S1 1
UDP C5 S1 1
UDP C6 S1 1
UDP O2 S1 1
UDP O4 S1 1
UDP "C1'" S1 1
UDP "C2'" S1 1
UDP "C3'" S1 1
UDP "C4'" S1 1
UDP "O4'" S1 1
UDP "O5'" F1 1
UDP PA F1 1
UDP O1A F1 1
UDP O2A F1 1
UDP O3A F1 1
UDP O3A F1 2
UDP PB F1 2
UDP O1B F1 2
UDP O2B F1 2
UDP O3B F1 2
UDP C5 F2 1
UDP C4 F2 1
UDP N3 F2 1
UDP C2 F2 1
UDP N1 F2 1
UDP C6 F2 1
UDP "C2'" F3 1
UDP "C3'" F3 1
UDP "C4'" F3 1
UDP "O4'" F3 1
UDP "C1'" F3 1
UDP "C5'" F3 1
UDP "O5'" F3 1
UDP "O3'" F3 1
UDP "O2'" F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id UDP
_pdbe_chem_comp_rdkit_properties.exactmw 404.002
_pdbe_chem_comp_rdkit_properties.amw 404.161
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 14
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 13
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 25
_pdbe_chem_comp_rdkit_properties.NumAtoms 39
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 16
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.556
_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 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 157.795
_pdbe_chem_comp_rdkit_properties.tpsa 217.840
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.818
_pdbe_chem_comp_rdkit_properties.CrippenMR 76.369
_pdbe_chem_comp_rdkit_properties.chi0v 12.977
_pdbe_chem_comp_rdkit_properties.chi1v 8.429
_pdbe_chem_comp_rdkit_properties.chi2v 4.037
_pdbe_chem_comp_rdkit_properties.chi3v 4.037
_pdbe_chem_comp_rdkit_properties.chi4v 2.602
_pdbe_chem_comp_rdkit_properties.chi0n 25.188
_pdbe_chem_comp_rdkit_properties.chi1n 11.996
_pdbe_chem_comp_rdkit_properties.chi2n 2.122
_pdbe_chem_comp_rdkit_properties.chi3n 2.122
_pdbe_chem_comp_rdkit_properties.chi4n 1.294
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.180
_pdbe_chem_comp_rdkit_properties.kappa1 8.231
_pdbe_chem_comp_rdkit_properties.kappa2 7.210
_pdbe_chem_comp_rdkit_properties.kappa3 5.151
_pdbe_chem_comp_rdkit_properties.Phi 2.374
#
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
UDP UniChem DrugBank DB03435
UDP UniChem 'Guide to Pharmacology' 1749
UDP UniChem 'KEGG LIGAND' C00015
UDP UniChem ChEBI 17659
UDP UniChem ZINC ZINC000004490939
UDP UniChem fdasrs 5G0F599A1Y
UDP UniChem HMDB HMDB0000295
UDP UniChem PubChem 146015339
UDP UniChem NMRShiftDB 60021032
UDP UniChem MetaboLights MTBLC17659
UDP UniChem BRENDA 128429
UDP UniChem BRENDA 21718
UDP UniChem BRENDA 247496
UDP UniChem BRENDA 26
UDP UniChem 'Probes And Drugs' PD048470
UDP UniChem BRENDA 91822
UDP UniChem SureChEMBL SCHEMBL4245
UDP UniChem 'PubChem TPHARMA' 14806010
UDP UniChem 'PubChem TPHARMA' 14854965
UDP UniChem PubChem 6031
UDP UniChem Nikkaji J4.595K
UDP UniChem BindingDb 50118239
UDP UniChem BindingDb 50403871
UDP UniChem BRENDA 49470
#
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
UDP N1 -2.912 0.179 -0.542 ETKDGv3 1
UDP C2 -2.245 -0.644 -1.525 ETKDGv3 2
UDP N3 -2.923 -0.981 -2.737 ETKDGv3 3
UDP C4 -4.261 -0.527 -2.939 ETKDGv3 4
UDP C5 -4.922 0.273 -1.900 ETKDGv3 5
UDP C6 -4.275 0.591 -0.775 ETKDGv3 6
UDP O2 -1.077 -1.074 -1.326 ETKDGv3 7
UDP O4 -4.874 -0.814 -4.002 ETKDGv3 8
UDP "C1'" -2.267 0.531 0.734 ETKDGv3 9
UDP "C2'" -2.253 -0.669 1.690 ETKDGv3 10
UDP "O2'" -3.010 -0.371 2.838 ETKDGv3 11
UDP "C3'" -0.783 -0.848 2.018 ETKDGv3 12
UDP "C4'" -0.166 0.471 1.566 ETKDGv3 13
UDP "O4'" -0.945 0.968 0.505 ETKDGv3 14
UDP "O3'" -0.573 -1.067 3.390 ETKDGv3 15
UDP "C5'" 1.285 0.300 1.106 ETKDGv3 16
UDP "O5'" 1.801 1.556 0.734 ETKDGv3 17
UDP PA 3.396 1.335 0.177 ETKDGv3 18
UDP O1A 3.954 2.688 -0.204 ETKDGv3 19
UDP O2A 4.330 0.663 1.426 ETKDGv3 20
UDP O3A 3.367 0.323 -1.194 ETKDGv3 21
UDP PB 4.967 -0.145 -1.536 ETKDGv3 22
UDP O1B 5.449 -1.132 -0.496 ETKDGv3 23
UDP O2B 4.994 -0.896 -3.052 ETKDGv3 24
UDP O3B 6.003 1.195 -1.571 ETKDGv3 25
UDP HN3 -2.448 -1.563 -3.463 ETKDGv3 26
UDP H5 -5.944 0.603 -2.045 ETKDGv3 27
UDP H6 -4.797 1.176 -0.027 ETKDGv3 28
UDP "H1'" -2.813 1.381 1.205 ETKDGv3 29
UDP "H2'" -2.651 -1.587 1.194 ETKDGv3 30
UDP "HO2'" -3.227 -1.238 3.270 ETKDGv3 31
UDP "H3'" -0.386 -1.703 1.421 ETKDGv3 32
UDP "H4'" -0.193 1.207 2.402 ETKDGv3 33
UDP "HO3'" 0.360 -1.393 3.485 ETKDGv3 34
UDP "H5'1" 1.873 -0.125 1.951 ETKDGv3 35
UDP "H5'2" 1.302 -0.407 0.245 ETKDGv3 36
UDP HOA2 5.222 1.087 1.343 ETKDGv3 37
UDP HOB2 5.952 -1.079 -3.227 ETKDGv3 38
UDP HOB3 5.689 1.735 -2.340 ETKDGv3 39
#