Chemical Components in the PDB

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A : Summary

Code

A

One-letter code

A

Molecule name

ADENOSINE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 5'-adenylic acid
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H14 N5 O7 P

Formal charge

0

Molecular weight

347.221 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
Canonical SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N

IUPAC InChI

InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1

IUPAC InChI key

UDMBCSSLTHHNCD-KQYNXXCUSA-N
A

wwPDB Information

Atom count

37 (23 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



A : Atoms of Molecule

Total Number of Atoms: 37
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OP3 O O3P N N Y 0 2.135 -1.141 -5.313
2 P P P N N N 0 1.024 -0.137 -4.723
3 OP1 O O1P N N N 0 1.633 1.19 -4.488
4 OP2 O O2P N N N 0 -0.183 0.0050 -5.778
5 O5' O O5* N N N 0 0.456 -0.72 -3.334
6 C5' C C5* N N N 0 -0.52 0.209 -2.863
7 C4' C C4* R N N 0 -1.101 -0.287 -1.538
8 O4' O O4* N N N 0 -0.064 -0.383 -0.538
9 C3' C C3* S N N 0 -2.105 0.739 -0.969
10 O3' O O3* N N N 0 -3.445 0.36 -1.287
11 C2' C C2* R N N 0 -1.874 0.684 0.558
12 O2' O O2* N N N 0 -3.065 0.271 1.231
13 C1' C C1* R N N 0 -0.755 -0.367 0.729
14 N9 N N9 N Y N 0 0.158 0.029 1.803
15 C8 C C8 N Y N 0 1.265 0.813 1.672
16 N7 N N7 N Y N 0 1.843 0.963 2.828
17 C5 C C5 N Y N 0 1.143 0.292 3.773
18 C6 C C6 N Y N 0 1.29 0.091 5.156
19 N6 N N6 N N N 0 2.344 0.664 5.846
20 N1 N N1 N Y N 0 0.391 -0.656 5.787
21 C2 C C2 N Y N 0 -0.617 -1.206 5.136
22 N3 N N3 N Y N 0 -0.792 -1.051 3.841
23 C4 C C4 N Y N 0 0.056 -0.32 3.126
24 HOP3 H 3HOP N N N 0 2.448 -0.755 -6.142
25 HOP2 H 2HOP N N N 0 -0.552 -0.879 -5.902
26 H5' H 1H5* N N N 0 -1.319 0.301 -3.599
27 H5'' H 2H5* N N N 0 -0.052 1.182 -2.712
28 H4' H H4* N N N 0 -1.586 -1.254 -1.677
29 H3' H H3* N N N 0 -1.89 1.736 -1.353
30 HO3' H H3T N N Y 0 -4.024 1.035 -0.908
31 H2' H H2* N N N 0 -1.543 1.654 0.93
32 HO2' H 2HO* N N N 0 -3.74 0.936 1.037
33 H1' H H1* N N N 0 -1.185 -1.346 0.94
34 H8 H H8 N N N 0 1.611 1.246 0.745
35 H61 H 1H6 N N N 0 2.432 0.522 6.801
36 H62 H 2H6 N N N 0 2.996 1.205 5.374
37 H2 H H2 N N N 0 -1.325 -1.807 5.688



A : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP3 P O P sing 1.61 N N
2 OP3 HOP3 O H sing 0.97 N N
3 P OP1 P O doub 1.48 N N
4 P OP2 P O sing 1.61 N N
5 P O5' P O sing 1.61 N N
6 OP2 HOP2 O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C5' H5' C H sing 1.09 N N
10 C5' H5'' C H sing 1.09 N N
11 C4' O4' C O sing 1.44 N N
12 C4' C3' C C sing 1.54 N N
13 C4' H4' C H sing 1.09 N N
14 O4' C1' O C sing 1.44 N N
15 C3' O3' C O sing 1.43 N N
16 C3' C2' C C sing 1.55 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 1.54 N N
21 C2' H2' C H sing 1.09 N N
22 O2' HO2' O H sing 0.97 N N
23 C1' N9 C N sing 1.46 N N
24 C1' H1' C H sing 1.09 N N
25 N9 C8 N C sing 1.36 N Y
26 N9 C4 N C sing 1.37 N Y
27 C8 N7 C N doub 1.3 N Y
28 C8 H8 C H sing 1.08 N N
29 N7 C5 N C sing 1.35 N Y
30 C5 C6 C C sing 1.41 N Y
31 C5 C4 C C doub 1.41 N Y
32 C6 N6 C N sing 1.38 N N
33 C6 N1 C N doub 1.33 N Y
34 N6 H61 N H sing 0.97 N N
35 N6 H62 N H sing 0.97 N N
36 N1 C2 N C sing 1.32 N Y
37 C2 N3 C N doub 1.32 N Y
38 C2 H2 C H sing 1.08 N N
39 N3 C4 N C sing 1.33 N Y



A : Used in PDB Entries

Total Number of PDB Entries: 27
Ligand Code PDB Entry ID Type Total Distinct
A 1bkx Open in New Window Bound ligand 1 1
A 1cvj Open in New Window Bound ligand 8 1
A 1exd Open in New Window Bound ligand 1 1
A 3fit Open in New Window Bound ligand 1 1
A 3j7y Open in New Window Bound ligand 1 1
A 3ra8 Open in New Window Bound ligand 1 1
A 3raa Open in New Window Bound ligand 1 1
A 4k9a Open in New Window Bound ligand 1 1
A 4k9b Open in New Window Bound ligand 1 1
A 4lfz Open in New Window Bound ligand 1 1
A 4m30 Open in New Window Bound ligand 2 1
A 4u3n Open in New Window Bound ligand 2 1
A 5d4d Open in New Window Bound ligand 1 1
A 5fdu Open in New Window Bound ligand 2 1
A 5fdv Open in New Window Bound ligand 1 1
A 5gtd Open in New Window Bound ligand 2 1
A 5lmo Open in New Window Bound ligand 3 1
A 5o4z Open in New Window Bound ligand 2 1
A 5xsp Open in New Window Bound ligand 4 1
A 6aek Open in New Window Bound ligand 1 1
A 6nmm Open in New Window Bound ligand 6 1
A 6nmn Open in New Window Bound ligand 2 1
A 6of6 Open in New Window Bound ligand 1 1
A 6qul Open in New Window Bound ligand 1 1
A 7bum Open in New Window Bound ligand 2 1
A 7kl3 Open in New Window Bound ligand 1 1
A 7oic Open in New Window Bound ligand 1 1