Chemical Components in the PDB

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ND7 : Summary

Code

ND7

One-letter code

X

Molecule name

5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine

Systematic names

ProgramVersionName
ACDLabs 12.01 5'-O-[(S)-amino(hydroxy)phosphoryl]adenosine
OpenEye OEToolkits 2.0.7 [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxyphosphonamidic acid

Formula

C10 H15 N6 O6 P

Formal charge

0

Molecular weight

346.236 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OP(OCC3C(C(O)C(n1cnc2c1ncnc2N)O3)O)(=O)N
SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](N)(O)=O)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(N)O)O)O)N
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](N)(O)=O)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(N)O)O)O)N

IUPAC InChI

InChI=1S/C10H15N6O6P/c11-8-5-9(14-2-13-8)16(3-15-5)10-7(18)6(17)4(22-10)1-21-23(12,19)20/h2-4,6-7,10,17-18H,1H2,(H2,11,13,14)(H3,12,19,20)/t4-,6-,7-,10-/m1/s1

IUPAC InChI key

LDEMREUBLBGZBO-KQYNXXCUSA-N
ND7

wwPDB Information

Atom count

38 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-05-10

Last modified at

2019-05-17

Status

Released

Obsoleted

Not Assigned



ND7 : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1A O O1 N N N 0 -5.162 2.116 -1.302
2 PA P P1 N N N 0 -4.866 1.015 -0.165
3 O2A O O2 N N N 0 -4.789 1.679 1.156
4 N3A N N1 N N N 0 -6.104 -0.124 -0.15
5 O5' O O3 N N N 0 -3.467 0.283 -0.479
6 C5' C C1 N N N 0 -2.822 -0.594 0.447
7 C4' C C2 R N N 0 -1.52 -1.114 -0.165
8 C3' C C3 S N N 0 -0.868 -2.161 0.766
9 O3' O O4 N N N 0 -1.18 -3.484 0.328
10 C2' C C4 R N N 0 0.647 -1.889 0.633
11 O2' O O5 N N N 0 1.317 -3.037 0.109
12 C4 C C6 N Y N 0 3.134 0.084 -0.315
13 C1' C C5 R N N 0 0.731 -0.711 -0.362
14 O4' O O6 N N N 0 -0.549 -0.05 -0.261
15 N9 N N2 N Y N 0 1.809 0.204 0.021
16 C5 C C7 N Y N 0 3.784 1.183 0.271
17 N7 N N3 N Y N 0 2.84 1.904 0.922
18 C8 C C8 N Y N 0 1.679 1.334 0.771
19 N3 N N4 N Y N 0 3.848 -0.789 -1.02
20 C2 C C9 N Y N 0 5.146 -0.628 -1.168
21 N1 N N5 N Y N 0 5.8 0.389 -0.637
22 C6 C C10 N Y N 0 5.171 1.311 0.083
23 N6 N N6 N N N 0 5.865 2.374 0.636
24 H1 H H1 N N N 0 -5.991 2.598 -1.176
25 H2 H H2 N N N 0 -6.177 -0.591 -1.041
26 H3 H H3 N N N 0 -5.975 -0.789 0.598
27 H4 H H4 N N N 0 -2.6 -0.052 1.366
28 H5 H H5 N N N 0 -3.48 -1.434 0.671
29 H7 H H7 N N N 0 -1.195 -2.011 1.795
30 H6 H H6 N N N 0 -1.71 -1.547 -1.148
31 H13 H H13 N N N 0 5.697 -1.355 -1.747
32 H8 H H8 N N N 0 -0.796 -4.181 0.877
33 H9 H H9 N N N 0 1.07 -1.608 1.598
34 H10 H H10 N N N 0 1.244 -3.824 0.667
35 H11 H H11 N N N 0 0.891 -1.081 -1.375
36 H12 H H12 N N N 0 0.751 1.702 1.183
37 H14 H H14 N N N 0 5.394 3.04 1.16
38 H15 H H15 N N N 0 6.822 2.451 0.499



ND7 : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2A PA O P doub 1.48 N N
2 N3A PA N P sing 1.68 N N
3 PA O5' P O sing 1.61 N N
4 PA O1A P O sing 1.61 N N
5 O5' C5' O C sing 1.43 N N
6 C5' C4' C C sing 1.53 N N
7 O3' C3' O C sing 1.43 N N
8 C4' C3' C C sing 1.55 N N
9 C4' O4' C O sing 1.44 N N
10 C3' C2' C C sing 1.54 N N
11 O4' C1' O C sing 1.44 N N
12 C1' C2' C C sing 1.54 N N
13 C1' N9 C N sing 1.46 N N
14 C2' O2' C O sing 1.43 N N
15 N9 C8 N C sing 1.36 N Y
16 N9 C4 N C sing 1.37 N Y
17 N3 C4 N C doub 1.33 N Y
18 N3 C2 N C sing 1.32 N Y
19 C8 N7 C N doub 1.3 N Y
20 C4 C5 C C sing 1.4 N Y
21 C2 N1 C N doub 1.32 N Y
22 N7 C5 N C sing 1.35 N Y
23 C5 C6 C C doub 1.41 N Y
24 N1 C6 N C sing 1.33 N Y
25 C6 N6 C N sing 1.38 N N
26 O1A H1 O H sing 0.97 N N
27 N3A H2 N H sing 1.01 N N
28 N3A H3 N H sing 1.01 N N
29 C5' H4 C H sing 1.09 N N
30 C5' H5 C H sing 1.09 N N
31 C4' H6 C H sing 1.09 N N
32 C3' H7 C H sing 1.09 N N
33 O3' H8 O H sing 0.97 N N
34 C2' H9 C H sing 1.09 N N
35 O2' H10 O H sing 0.97 N N
36 C1' H11 C H sing 1.09 N N
37 C8 H12 C H sing 1.08 N N
38 C2 H13 C H sing 1.08 N N
39 N6 H14 N H sing 0.97 N N
40 N6 H15 N H sing 0.97 N N



ND7 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
ND7 6om4 Open in New Window Bound ligand 2 1