Chemical Components in the PDB

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AKM : Summary

Code

AKM

One-letter code

X

Molecule name

[(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate

Synonyms

dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose (hydrated at C4)

Systematic names

ProgramVersionName
ACDLabs 12.01 (2R,4S,6R)-4-amino-5,5-dihydroxy-4,6-dimethyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
OpenEye OEToolkits 1.7.6 [(2R,4S,6R)-4-azanyl-4,6-dimethyl-5,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate

Formula

C17 H29 N3 O14 P2

Formal charge

0

Molecular weight

561.371 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)(O)C(N)(C3)C)C)O)O)C
SMILES CACTVS 3.370 C[CH]1O[CH](C[C](C)(N)C1(O)O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O
SMILES OpenEye OEToolkits 1.7.6 CC1C(C(CC(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)(C)N)(O)O
Canonical SMILES CACTVS 3.370 C[C@H]1O[C@@H](C[C@](C)(N)C1(O)O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@@H]1C([C@@](C[C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)(C)N)(O)O

IUPAC InChI

InChI=1S/C17H29N3O14P2/c1-8-6-20(15(23)19-14(8)22)12-4-10(21)11(32-12)7-30-35(26,27)34-36(28,29)33-13-5-16(3,18)17(24,25)9(2)31-13/h6,9-13,21,24-25H,4-5,7,18H2,1-3H3,(H,26,27)(H,28,29)(H,19,22,23)/t9-,10+,11-,12-,13-,16+/m1/s1

IUPAC InChI key

GACNZVKWDHTCBB-HHMBNNFFSA-N
AKM

wwPDB Information

Atom count

65 (36 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-04-29

Last modified at

2013-05-23

Status

Released

Obsoleted

Not Assigned



AKM : Atoms of Molecule

Total Number of Atoms: 65
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2P O O2P N N N 0 -0.38 1.543 2.171
2 P P P N N N 0 -0.14 2.007 0.648
3 O1P O O1P N N N 0 0.109 3.466 0.61
4 OPP O OPP N N N 0 1.133 1.229 0.044
5 P2 P P2 N N N 0 2.725 1.368 0.241
6 O3P O O3P N N N 0 3.033 1.513 1.681
7 O1 O O1 N N N 0 3.453 0.052 -0.334
8 C1 C C1 R N N 0 4.863 -0.176 -0.212
9 C2 C C2 N N N 0 5.337 -1.019 -1.396
10 C3 C C3 S N N 0 6.829 -1.313 -1.27
11 C3M C C3M N N N 0 7.643 -0.05 -1.562
12 N3 N N3 N N N 0 7.184 -2.323 -2.294
13 C4 C C4 N N N 0 7.183 -1.882 0.098
14 O4A O O4A N N N 0 6.865 -3.285 0.109
15 O4B O O4B N N N 0 8.604 -1.758 0.292
16 C5 C C5 R N N 0 6.473 -1.21 1.262
17 C6 C C6 N N N 0 7.237 0.027 1.736
18 O5 O O5 N N N 0 5.119 -0.893 0.991
19 O4P O O4P N N N 0 3.253 2.664 -0.555
20 O5' O O5* N N N 0 -1.446 1.663 -0.229
21 C5' C C5* N N N 0 -2.716 2.28 -0.01
22 C4' C C4* R N N 0 -3.731 1.727 -1.013
23 C3' C C3* S N N 0 -5.117 2.389 -0.807
24 O3' O O3* N N N 0 -5.211 3.614 -1.537
25 C2' C C2* N N N 0 -6.076 1.323 -1.391
26 C1' C C1* R N N 0 -5.256 0.019 -1.356
27 O4' O O4* N N N 0 -3.985 0.328 -0.761
28 N11 N N11 N N N 0 -5.953 -0.986 -0.55
29 C21 C C21 N N N 0 -6.126 -0.78 0.768
30 O21 O O21 N N N 0 -5.702 0.241 1.276
31 N31 N N31 N N N 0 -6.762 -1.686 1.533
32 C41 C C41 N N N 0 -7.239 -2.823 0.986
33 O41 O O41 N N N 0 -7.815 -3.643 1.677
34 C51 C C51 N N N 0 -7.063 -3.053 -0.4
35 C5A C C5A N N N 0 -7.585 -4.315 -1.037
36 C61 C C61 N N N 0 -6.426 -2.124 -1.145
37 H1 H H1 N N N 0 -0.549 0.596 2.272
38 H2 H H2 N N N 0 5.373 0.784 -0.203
39 H3 H H3 N N N 0 4.779 -1.957 -1.418
40 H4 H H4 N N N 0 5.149 -0.475 -2.325
41 H5 H H5 N N N 0 7.371 0.73 -0.851
42 H6 H H6 N N N 0 8.706 -0.272 -1.469
43 H7 H H7 N N N 0 7.431 0.292 -2.575
44 H8 H H8 N N N 0 6.986 -1.982 -3.223
45 H9 H H9 N N N 0 8.151 -2.6 -2.21
46 H11 H H11 N N N 0 7.099 -3.734 0.933
47 H12 H H12 N N N 0 8.916 -2.098 1.142
48 H13 H H13 N N N 0 6.476 -1.929 2.109
49 H14 H H14 N N N 0 6.778 0.411 2.647
50 H15 H H15 N N N 0 8.274 -0.241 1.937
51 H16 H H16 N N N 0 7.204 0.794 0.961
52 H17 H H17 N N N 0 3.085 2.637 -1.506
53 H18 H H18 N N N 0 -3.054 2.066 1.004
54 H19 H H19 N N N 0 -2.624 3.358 -0.143
55 H20 H H20 N N N 0 -3.38 1.875 -2.034
56 H21 H H21 N N N 0 -5.317 2.553 0.252
57 H22 H H22 N N N 0 -6.06 4.066 -1.44
58 H23 H H23 N N N 0 -6.967 1.23 -0.77
59 H24 H H24 N N N 0 -6.348 1.575 -2.416
60 H25 H H25 N N N 0 -5.111 -0.355 -2.37
61 H26 H H26 N N N 0 -6.879 -1.521 2.482
62 H27 H H27 N N N 0 -8.069 -4.931 -0.278
63 H28 H H28 N N N 0 -8.308 -4.059 -1.812
64 H29 H H29 N N N 0 -6.757 -4.868 -1.48
65 H30 H H30 N N N 0 -6.286 -2.28 -2.204



AKM : Chemical Bonds

Total Number of Bonds: 67
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O4A C4 O C sing 1.44 N N
2 C6 C5 C C sing 1.53 N N
3 O3P P2 O P doub 1.48 N N
4 C5 O5 C O sing 1.42 N N
5 C5 C4 C C sing 1.52 N N
6 O5 C1 O C sing 1.42 N N
7 C4 O4B C O sing 1.44 N N
8 C4 C3 C C sing 1.52 N N
9 O1 P2 O P sing 1.61 N N
10 O1 C1 O C sing 1.43 N N
11 N3 C3 N C sing 1.48 N N
12 P2 O4P P O sing 1.61 N N
13 P2 OPP P O sing 1.61 N N
14 C2 C1 C C sing 1.53 N N
15 C2 C3 C C sing 1.53 N N
16 C3 C3M C C sing 1.53 N N
17 O3' C3' O C sing 1.43 N N
18 OPP P O P sing 1.61 N N
19 C3' C4' C C sing 1.55 N N
20 C3' C2' C C sing 1.55 N N
21 P O1P P O doub 1.48 N N
22 P O2P P O sing 1.61 N N
23 P O5' P O sing 1.61 N N
24 C4' C5' C C sing 1.53 N N
25 C4' O4' C O sing 1.44 N N
26 C5' O5' C O sing 1.43 N N
27 C2' C1' C C sing 1.54 N N
28 O4' C1' O C sing 1.44 N N
29 C1' N11 C N sing 1.46 N N
30 O21 C21 O C doub 1.22 N N
31 N11 C21 N C sing 1.35 N N
32 N11 C61 N C sing 1.37 N N
33 C21 N31 C N sing 1.35 N N
34 C61 C51 C C doub 1.35 N N
35 N31 C41 N C sing 1.35 N N
36 C51 C41 C C sing 1.42 N N
37 C51 C5A C C sing 1.51 N N
38 C41 O41 C O doub 1.22 N N
39 O2P H1 O H sing 0.97 N N
40 C1 H2 C H sing 1.09 N N
41 C2 H3 C H sing 1.09 N N
42 C2 H4 C H sing 1.09 N N
43 C3M H5 C H sing 1.09 N N
44 C3M H6 C H sing 1.09 N N
45 C3M H7 C H sing 1.09 N N
46 N3 H8 N H sing 1.01 N N
47 N3 H9 N H sing 1.01 N N
48 O4A H11 O H sing 0.97 N N
49 O4B H12 O H sing 0.97 N N
50 C5 H13 C H sing 1.11 N N
51 C6 H14 C H sing 1.09 N N
52 C6 H15 C H sing 1.09 N N
53 C6 H16 C H sing 1.09 N N
54 O4P H17 O H sing 0.97 N N
55 C5' H18 C H sing 1.09 N N
56 C5' H19 C H sing 1.09 N N
57 C4' H20 C H sing 1.09 N N
58 C3' H21 C H sing 1.09 N N
59 O3' H22 O H sing 0.97 N N
60 C2' H23 C H sing 1.09 N N
61 C2' H24 C H sing 1.09 N N
62 C1' H25 C H sing 1.09 N N
63 N31 H26 N H sing 0.97 N N
64 C5A H27 C H sing 1.09 N N
65 C5A H28 C H sing 1.09 N N
66 C5A H29 C H sing 1.09 N N
67 C61 H30 C H sing 1.08 N N



AKM : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
AKM 4kcf Open in New Window Bound ligand 1 1