Chemical Components in the PDB

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GMV : Summary

Code

GMV

One-letter code

X

Molecule name

GUANOSINE-5'-PHOSPHOVANADATE

Systematic names

ProgramVersionName
ACDLabs 12.01 vanadium(5+) hydroxide 5'-O-[(R)-hydroxyphosphinato]guanosine (1:4:1)
OpenEye OEToolkits 1.9.2 [[(2R,3S,4R,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-tetrakis(oxidanyl)vanadium

Formula

C10 H17 N5 O12 P V

Formal charge

0

Molecular weight

481.184 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O[V](O)(O)(O)O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[V](O)(O)(O)O)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 1.9.2 c1nc2c(n1C3C(C(C(O3)COP(=O)(O)O[V](O)(O)(O)O)O)O)N=C(NC2=O)N
Canonical SMILES CACTVS 3.385 NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[V](O)(O)(O)O)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.9.2 c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[V](O)(O)(O)O)O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C10H14N5O8P.4H2O.V/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(23-9)1-22-24(19,20)21;;;;;/h2-3,5-6,9,16-17H,1H2,(H2,19,20,21)(H3,11,13,14,18);4*1H2;/q;;;;;+5/p-5/t3-,5-,6-,9-;;;;;/m1...../s1

IUPAC InChI key

BCICKRMJBANRAL-LTPGDGGNSA-I
GMV

wwPDB Information

Atom count

46 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-06-04

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



GMV : Atoms of Molecule

Total Number of Atoms: 46
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 VB V VB N N N 0 5.692 -0.854 -0.381
2 O1B O O1B N N N 0 6.163 0.907 -0.136
3 O2B O O2B N N N 0 5.01 -1.829 1.023
4 O3B O O3B N N N 0 5.901 -1.641 -2.031
5 O4B O O4B N N N 0 7.394 -1.375 0.083
6 PA P PA N N N 0 3.215 0.48 0.308
7 O1A O O1A N N N 0 3.973 1.708 0.637
8 O2A O O2A N N N 0 3.089 -0.441 1.622
9 O3A O O3A N N N 0 3.989 -0.334 -0.846
10 O5' O O5' N N N 0 1.745 0.88 -0.211
11 C5' C C5' N N N 0 0.849 1.698 0.543
12 C4' C C4' R N N 0 -0.455 1.881 -0.237
13 O4' O O4' N N N 0 -1.141 0.622 -0.343
14 C3' C C3' S N N 0 -1.386 2.849 0.518
15 O3' O O3' N N N 0 -1.68 3.991 -0.288
16 C2' C C2' R N N 0 -2.67 2.02 0.771
17 O2' O O2' N N N 0 -3.839 2.815 0.562
18 C1' C C1' R N N 0 -2.556 0.909 -0.303
19 N9 N N9 N Y N 0 -3.312 -0.279 0.102
20 C8 C C8 N Y N 0 -2.832 -1.335 0.822
21 N7 N N7 N Y N 0 -3.776 -2.212 1.0
22 C5 C C5 N Y N 0 -4.914 -1.773 0.408
23 C6 C C6 N N N 0 -6.223 -2.295 0.281
24 O6 O O6 N N N 0 -6.516 -3.372 0.772
25 N1 N N1 N N N 0 -7.14 -1.57 -0.396
26 C2 C C2 N N N 0 -6.801 -0.367 -0.94
27 N2 N N2 N N N 0 -7.753 0.348 -1.622
28 N3 N N3 N N N 0 -5.589 0.129 -0.829
29 C4 C C4 N Y N 0 -4.63 -0.53 -0.168
30 H1B H H1B N N N 0 6.51 1.336 -0.93
31 H2B H H2B N N N 0 4.792 -2.744 0.798
32 H3B H H3B N N N 0 6.763 -2.06 -2.161
33 H4B H H4B N N N 0 7.532 -2.332 0.065
34 H2A H H2A N N N 0 2.603 -1.265 1.48
35 H5'1 H H5'1 N N N 0 0.636 1.219 1.499
36 H5'2 H H5'2 N N N 0 1.306 2.672 0.719
37 H4' H H4' N N N 0 -0.24 2.27 -1.232
38 H3' H H3' N N N 0 -0.935 3.154 1.462
39 H1' H H1' N N N 0 -2.901 1.274 -1.27
40 HA H HA N N N 0 -2.263 4.634 0.139
41 H2' H H2' N N N 0 -2.666 1.594 1.775
42 HB H HB N N N 0 -3.908 3.577 1.153
43 H8 H H8 N N N 0 -1.821 -1.428 1.188
44 H1 H H1 N N N 0 -8.044 -1.907 -0.496
45 H21N H H21N N N N 0 -8.653 -0.005 -1.712
46 H22N H H22N N N N 0 -7.527 1.206 -2.015



GMV : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 VB O1B V O sing 1.84 N N
2 VB O2B V O sing 1.84 N N
3 VB O3B V O sing 1.84 N N
4 VB O4B V O sing 1.84 N N
5 VB O3A V O sing 1.84 N N
6 O3A PA O P sing 1.61 N N
7 PA O1A P O doub 1.48 N N
8 PA O2A P O sing 1.61 N N
9 PA O5' P O sing 1.61 N N
10 O5' C5' O C sing 1.43 N N
11 C5' C4' C C sing 1.53 N N
12 C4' O4' C O sing 1.44 N N
13 C4' C3' C C sing 1.54 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 C2' O2' C O sing 1.43 N N
18 C2' C1' C C sing 1.55 N N
19 C1' N9 C N sing 1.47 N N
20 N9 C8 N C sing 1.37 N Y
21 N9 C4 N C sing 1.37 N Y
22 C8 N7 C N doub 1.3 N Y
23 N7 C5 N C sing 1.36 N Y
24 C5 C6 C C sing 1.41 N N
25 C5 C4 C C doub 1.4 N Y
26 C6 O6 C O doub 1.22 N N
27 C6 N1 C N sing 1.35 N N
28 N1 C2 N C sing 1.36 N N
29 C2 N2 C N sing 1.37 N N
30 C2 N3 C N doub 1.31 N N
31 C4 N3 C N sing 1.34 N N
32 O1B H1B O H sing 0.97 N N
33 O2B H2B O H sing 0.97 N N
34 O3B H3B O H sing 0.97 N N
35 O4B H4B O H sing 0.97 N N
36 O2A H2A O H sing 0.97 N N
37 C5' H5'1 C H sing 1.09 N N
38 C5' H5'2 C H sing 1.09 N N
39 C4' H4' C H sing 1.09 N N
40 C3' H3' C H sing 1.09 N N
41 C1' H1' C H sing 1.09 N N
42 O3' HA O H sing 0.97 N N
43 C2' H2' C H sing 1.09 N N
44 O2' HB O H sing 0.97 N N
45 C8 H8 C H sing 1.08 N N
46 N1 H1 N H sing 0.97 N N
47 N2 H21N N H sing 0.97 N N
48 N2 H22N N H sing 0.97 N N



GMV : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
GMV 4brl Open in New Window Bound ligand 2 1