Chemical Components in the PDB

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3GP : Summary

Code

3GP

One-letter code

X

Molecule name

GUANOSINE-3'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 3'-guanylic acid
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate

Formula

C10 H14 N5 O8 P

Formal charge

0

Molecular weight

363.221 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1c2ncn(c2N=C(N)N1)C3OC(C(OP(=O)(O)O)C3O)CO
SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO)[CH](O[P](O)(O)=O)[CH]3O
SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1C3C(C(C(O3)CO)OP(=O)(O)O)O)N=C(NC2=O)N
Canonical SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[C@@H](O[P](O)(O)=O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)OP(=O)(O)O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C10H14N5O8P/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-5(17)6(3(1-16)22-9)23-24(19,20)21/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1

IUPAC InChI key

ZDPUTNZENXVHJC-UUOKFMHZSA-N
3GP

wwPDB Information

Atom count

38 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



3GP : 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 P P P N N N 0 1.075 0.411 4.147
2 O1P O O1P N N N 0 -0.2 0.586 4.877
3 O2P O O2P N N N 0 2.176 -0.224 5.134
4 O3P O O3P N N N 0 1.591 1.841 3.616
5 O5' O O5* N N N 0 -3.623 -1.309 2.616
6 C5' C C5* N N N 0 -2.479 -0.484 2.845
7 C4' C C4* R N N 0 -1.359 -0.887 1.885
8 O4' O O4* N N N 0 -1.776 -0.695 0.516
9 C3' C C3* S N N 0 -0.137 0.041 2.059
10 O3' O O3* N N N 0 0.844 -0.574 2.894
11 C2' C C2* R N N 0 0.407 0.22 0.622
12 O2' O O2* N N N 0 1.743 -0.276 0.528
13 C1' C C1* R N N 0 -0.553 -0.619 -0.247
14 N9 N N9 N Y N 0 -0.793 0.047 -1.53
15 C8 C C8 N Y N 0 -1.767 0.966 -1.792
16 N7 N N7 N Y N 0 -1.69 1.348 -3.033
17 C5 C C5 N Y N 0 -0.666 0.7 -3.64
18 C6 C C6 N N N 0 -0.127 0.715 -4.948
19 O6 O O6 N N N 0 -0.605 1.431 -5.812
20 N1 N N1 N N N 0 0.932 -0.078 -5.214
21 C2 C C2 N N N 0 1.454 -0.879 -4.242
22 N2 N N2 N N N 0 2.528 -1.679 -4.543
23 N3 N N3 N N N 0 0.963 -0.902 -3.023
24 C4 C C4 N Y N 0 -0.082 -0.138 -2.684
25 HOP2 H 2HOP N N N 0 2.283 0.395 5.869
26 HOP3 H 3HOP N N N 0 2.421 1.682 3.147
27 HO5' H *HO5 N N N 0 -4.304 -1.023 3.24
28 H5'1 H 1H5* N N N 0 -2.14 -0.611 3.873
29 H5'2 H 2H5* N N N 0 -2.744 0.559 2.676
30 H4' H H4* N N N 0 -1.072 -1.926 2.051
31 H3' H H3* N N N 0 -0.443 1.001 2.475
32 H2' H H2* N N N 0 0.369 1.269 0.328
33 HO2' H *HO2 N N N 0 2.029 -0.138 -0.385
34 H1' H H1* N N N 0 -0.144 -1.616 -0.409
35 H8 H H8 N N N 0 -2.493 1.323 -1.076
36 HN1 H HN1 N N N 0 1.319 -0.085 -6.104
37 HN21 H 1HN2 N N N 0 2.913 -2.251 -3.861
38 HN22 H 2HN2 N N N 0 2.899 -1.676 -5.439



3GP : 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 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 O3' 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 O5' C5' O C sing 1.43 N N
8 O5' HO5' O H sing 0.97 N N
9 C5' C4' C C sing 1.53 N N
10 C5' H5'1 C H sing 1.09 N N
11 C5' H5'2 C H sing 1.09 N N
12 C4' O4' C O sing 1.44 N N
13 C4' C3' C C sing 1.54 N N
14 C4' H4' C H sing 1.09 N N
15 O4' C1' O C sing 1.44 N N
16 C3' O3' C O sing 1.43 N N
17 C3' C2' C C sing 1.55 N N
18 C3' H3' C H sing 1.09 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 1.47 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 1.36 N Y
30 C5 C6 C C sing 1.41 N N
31 C5 C4 C C doub 1.4 N Y
32 C6 O6 C O doub 1.22 N N
33 C6 N1 C N sing 1.35 N N
34 N1 C2 N C sing 1.36 N N
35 N1 HN1 N H sing 0.97 N N
36 C2 N2 C N sing 1.37 N N
37 C2 N3 C N doub 1.31 N N
38 N2 HN21 N H sing 0.97 N N
39 N2 HN22 N H sing 0.97 N N
40 N3 C4 N C sing 1.34 N N



3GP : Used in PDB Entries

Total Number of PDB Entries: 22
Ligand Code PDB Entry ID Type Total Distinct
3GP 1goy Open in New Window Bound ligand 1 1
3GP 1lov Open in New Window Bound ligand 1 1
3GP 1low Open in New Window Bound ligand 1 1
3GP 1loy Open in New Window Bound ligand 1 1
3GP 1rga Open in New Window Bound ligand 1 1
3GP 1rgc Open in New Window Bound ligand 2 1
3GP 1rls Open in New Window Bound ligand 1 1
3GP 1rms Open in New Window Bound ligand 1 1
3GP 1xz8 Open in New Window Bound ligand 1 1
3GP 2gsp Open in New Window Bound ligand 1 1
3GP 2sar Open in New Window Bound ligand 1 1
3GP 3d4a Open in New Window Bound ligand 1 1
3GP 3dh2 Open in New Window Bound ligand 4 1
3GP 3gsp Open in New Window Bound ligand 1 1
3GP 3wr2 Open in New Window Bound ligand 6 1
3GP 4gsp Open in New Window Bound ligand 1 1
3GP 4hi6 Open in New Window Bound ligand 2 1
3GP 4w8x Open in New Window Bound ligand 1 1
3GP 5gsp Open in New Window Bound ligand 1 1
3GP 6gsp Open in New Window Bound ligand 1 1
3GP 8iy1 Open in New Window Bound ligand 6 1
3GP 8iy2 Open in New Window Bound ligand 4 1