Chemical Components in the PDB

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00A : Summary

Code

00A

One-letter code

A

Molecule name

5'-O-[(S)-{[(4-chlorophenyl)carbonyl]oxy}(hydroxy)phosphoryl]adenosine

Systematic names

ProgramVersionName
ACDLabs 10.04 5'-O-[(S)-{[(4-chlorophenyl)carbonyl]oxy}(hydroxy)phosphoryl]adenosine
OpenEye OEToolkits 1.5.0 [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] 4-chlorobenzoate

Formula

C17 H17 Cl N5 O8 P

Formal charge

0

Molecular weight

485.772 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 Clc1ccc(cc1)C(=O)OP(=O)(O)OCC4OC(n3cnc2c(ncnc23)N)C(O)C4O
SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)OC(=O)c4ccc(Cl)cc4)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1C(=O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)Cl
Canonical SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)OC(=O)c4ccc(Cl)cc4)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1C(=O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)Cl

IUPAC InChI

InChI=1S/C17H17ClN5O8P/c18-9-3-1-8(2-4-9)17(26)31-32(27,28)29-5-10-12(24)13(25)16(30-10)23-7-22-11-14(19)20-6-21-15(11)23/h1-4,6-7,10,12-13,16,24-25H,5H2,(H,27,28)(H2,19,20,21)/t10-,12-,13-,16-/m1/s1

IUPAC InChI key

RVDNKWBGRIIRML-XNIJJKJLSA-N
00A

wwPDB Information

Atom count

49 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

Yes

Standard parent

A

Defined at

2008-04-28

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



00A : Atoms of Molecule

Total Number of Atoms: 49
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 -2.658 -3.412 0.132
2 P P P S N N 0 -2.103 -1.962 0.559
3 O1P O O1P N N N 0 -1.97 -1.899 2.032
4 O3P O O3P N N N 0 -3.132 -0.827 0.064
5 CC C CC N N N 0 -4.358 -0.827 0.622
6 C1C C C1C N Y N 0 -5.354 0.185 0.217
7 C2C C C2C N Y N 0 -6.626 0.188 0.794
8 C3C C C3C N Y N 0 -7.551 1.136 0.412
9 C4C C C4C N Y N 0 -7.222 2.084 -0.543
10 CL4A CL CL4A N N N 0 -8.392 3.274 -1.02
11 C5C C C5C N Y N 0 -5.962 2.086 -1.119
12 C6C C C6C N Y N 0 -5.026 1.148 -0.74
13 O2 O O2 N N N 0 -4.644 -1.66 1.459
14 O5' O O5' N N N 0 -0.665 -1.716 -0.121
15 C5' C C5' N N N 0 0.49 -2.495 0.199
16 C4' C C4' R N N 0 1.682 -2.0 -0.623
17 C3' C C3' S N N 0 2.922 -2.882 -0.358
18 O3' O O3' N N N 0 3.073 -3.857 -1.393
19 C2' C C2' R N N 0 4.102 -1.886 -0.373
20 O2' O O2' N N N 0 5.022 -2.214 -1.416
21 C1' C C1' R N N 0 3.436 -0.519 -0.645
22 O4' O O4' N N N 0 2.071 -0.676 -0.197
23 N9 N N9 N Y N 0 4.106 0.536 0.12
24 C4 C C4 N Y N 0 5.227 1.229 -0.263
25 C5 C C5 N Y N 0 5.5 2.131 0.78
26 N7 N N7 N Y N 0 4.549 1.944 1.727
27 C8 C C8 N Y N 0 3.727 1.013 1.339
28 C6 C C6 N Y N 0 6.612 2.979 0.65
29 N6 N N6 N N N 0 6.931 3.887 1.644
30 N1 N N1 N Y N 0 7.352 2.889 -0.451
31 C2 C C2 N Y N 0 7.055 2.026 -1.405
32 N3 N N3 N Y N 0 6.024 1.211 -1.326
33 HO2P H HO2P N N N 0 -2.77 -3.525 -0.822
34 H2C H H2C N N N 0 -6.884 -0.551 1.538
35 H3C H H3C N N N 0 -8.535 1.139 0.857
36 H5C H H5C N N N 0 -5.711 2.828 -1.863
37 H6C H H6C N N N 0 -4.042 1.154 -1.187
38 H5' H H5' N N N 0 0.714 -2.394 1.26
39 H5'A H H5'A N N N 0 0.298 -3.542 -0.034
40 H4' H H4' N N N 0 1.436 -2.0 -1.685
41 H3' H H3' N N N 0 2.844 -3.368 0.614
42 HO3' H HO3' N N N 0 3.836 -4.439 -1.276
43 H2' H H2' N N N 0 4.608 -1.879 0.593
44 HO2' H HO2' N N N 0 5.424 -3.089 -1.325
45 H1' H H1' N N N 0 3.463 -0.289 -1.71
46 H8 H H8 N N N 0 2.873 0.667 1.902
47 HN6 H HN6 N N N 0 6.384 3.943 2.443
48 HN6A H HN6A N N N 0 7.701 4.467 1.543
49 H2 H H2 N N N 0 7.683 1.985 -2.283



00A : Chemical Bonds

Total Number of Bonds: 52
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O2P P O sing 1.61 N N
2 O2P HO2P O H sing 0.97 N N
3 O5' P O P sing 1.61 N N
4 P O1P P O doub 1.48 N N
5 P O3P P O sing 1.61 N N
6 CC O3P C O sing 1.35 N N
7 O2 CC O C doub 1.22 N N
8 CC C1C C C sing 1.48 N N
9 C6C C1C C C doub 1.4 N Y
10 C1C C2C C C sing 1.4 N Y
11 C2C C3C C C doub 1.38 N Y
12 C2C H2C C H sing 1.08 N N
13 C4C C3C C C sing 1.39 N Y
14 C3C H3C C H sing 1.08 N N
15 C5C C4C C C doub 1.39 N Y
16 C4C CL4A C CL sing 1.74 N N
17 C6C C5C C C sing 1.38 N Y
18 C5C H5C C H sing 1.08 N N
19 C6C H6C C H sing 1.08 N N
20 C5' O5' C O sing 1.43 N N
21 C4' C5' C C sing 1.53 N N
22 C5' H5' C H sing 1.09 N N
23 C5' H5'A C H sing 1.09 N N
24 O4' C4' O C sing 1.44 N N
25 C3' C4' C C sing 1.54 N N
26 C4' H4' C H sing 1.09 N N
27 C2' C3' C C sing 1.54 N N
28 O3' C3' O C sing 1.43 N N
29 C3' H3' C H sing 1.09 N N
30 O3' HO3' O H sing 0.97 N N
31 O2' C2' O C sing 1.43 N N
32 C1' C2' C C sing 1.54 N N
33 C2' H2' C H sing 1.09 N N
34 O2' HO2' O H sing 0.97 N N
35 C1' N9 C N sing 1.47 N N
36 C1' O4' C O sing 1.45 N N
37 C1' H1' C H sing 1.09 N N
38 C4 N9 C N sing 1.37 N Y
39 N9 C8 N C sing 1.36 N Y
40 N3 C4 N C doub 1.33 N Y
41 C4 C5 C C sing 1.41 N Y
42 C6 C5 C C doub 1.4 N Y
43 C5 N7 C N sing 1.36 N Y
44 C8 N7 C N doub 1.3 N Y
45 C8 H8 C H sing 1.08 N N
46 N1 C6 N C sing 1.33 N Y
47 C6 N6 C N sing 1.38 N N
48 N6 HN6 N H sing 0.97 N N
49 N6 HN6A N H sing 0.97 N N
50 C2 N1 C N doub 1.32 N Y
51 C2 N3 C N sing 1.32 N Y
52 C2 H2 C H sing 1.08 N N



00A : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
00A 3cw8 Open in New Window Bound ligand 1 1