Chemical Components in the PDB

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P2P : Summary

Code

P2P

One-letter code

X

Molecule name

N7-(5'-PHOSPHO-ALPHA-RIBOSYL)-2-HYDROXYPURINE

Systematic names

ProgramVersionName
ACDLabs 10.04 7-(5-O-phosphono-alpha-D-ribofuranosyl)-7H-purin-2-ol
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5S)-3,4-dihydroxy-5-(2-hydroxypurin-7-yl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H13 N4 O8 P

Formal charge

0

Molecular weight

348.206 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC3OC(n2cnc1nc(O)ncc12)C(O)C3O
SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2cnc3nc(O)ncc23
SMILES OpenEye OEToolkits 1.5.0 c1c2c(ncn2C3C(C(C(O3)COP(=O)(O)O)O)O)nc(n1)O
Canonical SMILES CACTVS 3.341 O[C@H]1[C@@H](O)[C@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3nc(O)ncc23
Canonical SMILES OpenEye OEToolkits 1.5.0 c1c2c(ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)nc(n1)O

IUPAC InChI

InChI=1S/C10H13N4O8P/c15-6-5(2-21-23(18,19)20)22-9(7(6)16)14-3-12-8-4(14)1-11-10(17)13-8/h1,3,5-7,9,15-16H,2H2,(H,11,13,17)(H2,18,19,20)/t5-,6-,7-,9+/m1/s1

IUPAC InChI key

BVZASCINAVSQNO-PULFBKJNSA-N
P2P

wwPDB Information

Atom count

36 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2001-07-10

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



P2P : Atoms of Molecule

Total Number of Atoms: 36
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P N N N 0 -0.668 -0.108 -4.849
2 O1P O O1P N N N 0 0.242 -1.186 -5.293
3 O2P O O2P N N N 0 -2.14 -0.369 -5.448
4 O3P O O3P N N N 0 -0.118 1.31 -5.377
5 O6' O O6* N N N 0 -0.738 -0.091 -3.241
6 C5' C C5* N N N 0 0.591 0.142 -2.772
7 C4' C C4* R N N 0 0.595 0.17 -1.243
8 O5' O O5* N N N 0 0.157 -1.103 -0.715
9 C3' C C3* S N N 0 2.032 0.344 -0.705
10 O3' O O3* N N N 0 2.278 1.711 -0.367
11 C2' C C2* R N N 0 2.073 -0.541 0.559
12 O2' O O2* N N N 0 2.349 0.25 1.717
13 C1' C C1* S N N 0 0.654 -1.147 0.639
14 C8 C C8 N Y N 0 -1.099 0.585 1.139
15 N9 N N9 N Y N 0 -1.677 1.109 2.183
16 C4 C C4 N Y N 0 -1.182 0.554 3.305
17 C5 C C5 N Y N 0 -0.223 -0.394 2.901
18 N7 N N7 N Y N 0 -0.194 -0.342 1.522
19 N3 N N3 N Y N 0 -1.413 0.716 4.609
20 C2 C C2 N Y N 0 -0.748 0.001 5.498
21 N1 N N1 N Y N 0 0.163 -0.893 5.147
22 C6 C C6 N Y N 0 0.452 -1.115 3.873
23 O11 O O11 N N N 0 -1.006 0.19 6.815
24 HOP2 H 2HOP N N N 0 -2.054 -0.371 -6.411
25 HOP3 H 3HOP N N N 0 -0.739 1.983 -5.067
26 H5'1 H 1H5* N N N 0 0.947 1.099 -3.154
27 H5'2 H 2H5* N N N 0 1.245 -0.654 -3.123
28 H4' H H4* N N N 0 -0.045 0.973 -0.877
29 H3' H H3* N N N 0 2.759 -0.003 -1.438
30 HO3' H *HO3 N N N 0 3.176 1.753 -0.01
31 H2' H H2* N N N 0 2.819 -1.329 0.45
32 HO2' H *HO2 N N N 0 3.219 0.648 1.582
33 H1' H H1* N N N 0 0.7 -2.176 0.994
34 H8 H H8 N N N 0 -1.312 0.854 0.115
35 H6 H H6 N N N 0 1.197 -1.847 3.598
36 HO11 H HO11 N N N 0 -1.714 -0.424 7.051



P2P : Chemical Bonds

Total Number of Bonds: 38
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O1P P O doub 1.48 N N
2 P O2P P O sing 1.61 N N
3 P O3P P O sing 1.61 N N
4 P O6' P O sing 1.61 N N
5 O2P HOP2 O H sing 0.97 N N
6 O3P HOP3 O H sing 0.97 N N
7 O6' C5' O C sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C5' H5'1 C H sing 1.09 N N
10 C5' H5'2 C H sing 1.09 N N
11 C4' O5' C O sing 1.45 N N
12 C4' C3' C C sing 1.54 N N
13 C4' H4' C H sing 1.09 N N
14 O5' C1' O C sing 1.44 N N
15 C3' O3' C O sing 1.43 N N
16 C3' C2' C C sing 1.54 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HO3' O H sing 0.97 N N
19 C2' O2' C O sing 1.43 N N
20 C2' C1' C C sing 1.55 N N
21 C2' H2' C H sing 1.09 N N
22 O2' HO2' O H sing 0.97 N N
23 C1' N7 C N sing 1.47 N N
24 C1' H1' C H sing 1.09 N N
25 C8 N9 C N doub 1.3 N Y
26 C8 N7 C N sing 1.35 N Y
27 C8 H8 C H sing 1.08 N N
28 N9 C4 N C sing 1.35 N Y
29 C4 C5 C C doub 1.41 N Y
30 C4 N3 C N sing 1.33 N Y
31 C5 N7 C N sing 1.38 N Y
32 C5 C6 C C sing 1.39 N Y
33 N3 C2 N C doub 1.32 N Y
34 C2 N1 C N sing 1.32 N Y
35 C2 O11 C O sing 1.36 N N
36 N1 C6 N C doub 1.33 N Y
37 C6 H6 C H sing 1.08 N N
38 O11 HO11 O H sing 0.97 N N



P2P : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
P2P 1jhr Open in New Window Bound ligand 1 1