Chemical Components in the PDB

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DG : Summary

Code

DG

One-letter code

G

Molecule name

2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-deoxy-5'-guanylic acid
OpenEye OEToolkits 1.5.0 [(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-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=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3)COP(=O)(O)O
SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C(NC2=O)N
Canonical SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1

IUPAC InChI key

LTFMZDNNPPEQNG-KVQBGUIXSA-N
DG

wwPDB Information

Atom count

37 (23 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

No

Standard parent

Not Assigned

Defined at

2001-06-01

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



DG : 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 -1.603 -1.547 5.624
2 P P P N N N 0 -0.818 -0.321 4.935
3 OP1 O O1P N N N 0 -1.774 0.766 4.63
4 OP2 O O2P N N N 0 0.312 0.224 5.941
5 O5' O O5* N N N 0 -0.126 -0.826 3.572
6 C5' C C5* N N N 0 0.55 0.3 3.011
7 C4' C C4* R N N 0 1.233 -0.113 1.706
8 O4' O O4* N N N 0 0.253 -0.471 0.705
9 C3' C C3* S N N 0 1.976 1.091 1.073
10 O3' O O3* N N N 0 3.294 1.218 1.612
11 C2' C C2* N N N 0 2.026 0.692 -0.421
12 C1' C C1* R N N 0 0.897 -0.345 -0.573
13 N9 N N9 N Y N 0 -0.068 0.111 -1.575
14 C8 C C8 N Y N 0 -1.172 0.877 -1.341
15 N7 N N7 N Y N 0 -1.804 1.094 -2.458
16 C5 C C5 N Y N 0 -1.145 0.482 -3.472
17 C6 C C6 N N N 0 -1.361 0.377 -4.866
18 O6 O O6 N N N 0 -2.321 0.914 -5.391
19 N1 N N1 N N N 0 -0.473 -0.327 -5.601
20 C2 C C2 N N N 0 0.593 -0.928 -5.003
21 N2 N N2 N N N 0 1.474 -1.643 -5.774
22 N3 N N3 N N N 0 0.804 -0.839 -3.709
23 C4 C C4 N Y N 0 -0.027 -0.152 -2.917
24 HOP3 H 3HOP N N N 0 -2.002 -1.203 6.435
25 HOP2 H 2HOP N N N 0 0.913 -0.513 6.114
26 H5' H 1H5* N N N 0 1.299 0.661 3.715
27 H5'' H 2H5* N N N 0 -0.17 1.093 2.808
28 H4' H H4* N N N 0 1.921 -0.94 1.879
29 H3' H H3* N N N 0 1.411 2.013 1.211
30 HO3' H H3T N N Y 0 3.732 1.921 1.114
31 H2' H 1H2* N N N 0 2.99 0.246 -0.665
32 H2'' H 2H2* N N N 0 1.834 1.559 -1.053
33 H1' H H1* N N N 0 1.316 -1.306 -0.873
34 H8 H H8 N N N 0 -1.477 1.248 -0.373
35 H1 H H1 N N N 0 -0.601 -0.413 -6.559
36 H21 H 1H2 N N N 0 2.24 -2.073 -5.363
37 H22 H 2H2 N N N 0 1.329 -1.722 -6.73



DG : 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 1.45 N N
12 C4' C3' C C sing 1.55 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' C1' C C sing 1.54 N N
20 C2' H2' C H sing 1.09 N N
21 C2' H2'' C H sing 1.09 N N
22 C1' N9 C N sing 1.46 N N
23 C1' H1' C H sing 1.09 N N
24 N9 C8 N C sing 1.36 N Y
25 N9 C4 N C sing 1.37 N Y
26 C8 N7 C N doub 1.3 N Y
27 C8 H8 C H sing 1.08 N N
28 N7 C5 N C sing 1.36 N Y
29 C5 C6 C C sing 1.41 N N
30 C5 C4 C C doub 1.4 N Y
31 C6 O6 C O doub 1.22 N N
32 C6 N1 C N sing 1.35 N N
33 N1 C2 N C sing 1.36 N N
34 N1 H1 N H sing 0.97 N N
35 C2 N2 C N sing 1.37 N N
36 C2 N3 C N doub 1.31 N N
37 N2 H21 N H sing 0.97 N N
38 N2 H22 N H sing 0.97 N N
39 N3 C4 N C sing 1.34 N N



DG : Used in PDB Entries

Total Number of PDB Entries: 10
Ligand Code PDB Entry ID Type Total Distinct
DG 2br0 Open in New Window Bound ligand 1 1
DG 2c28 Open in New Window Bound ligand 1 1
DG 2xjb Open in New Window Bound ligand 1 1
DG 3bbb Open in New Window Bound ligand 4 1
DG 4dsi Open in New Window Bound ligand 1 1
DG 6kqd Open in New Window Bound ligand 2 1
DG 6txr Open in New Window Bound ligand 22 1
DG 6wph Open in New Window Bound ligand 1 1
DG 6z9p Open in New Window Bound ligand 1 1
DG 6z9r Open in New Window Bound ligand 1 1