Chemical Components in the PDB

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TGP : Summary

Code

TGP

One-letter code

G

Molecule name

5'-THIO-2'-DEOXY-GUANOSINE PHOSPHONIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-deoxy-5'-S-phosphono-5'-thioguanosine
OpenEye OEToolkits 1.5.0 [(2S,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methylsulfanylphosphonic acid

Formula

C10 H14 N5 O6 P S

Formal charge

0

Molecular weight

363.287 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)SCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CS[P](O)(O)=O)O3
SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1C3CC(C(O3)CSP(=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](CS[P](O)(O)=O)O3
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CSP(=O)(O)O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C10H14N5O6PS/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(21-6)2-23-22(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

AHOKECUHLPOZOT-KVQBGUIXSA-N
TGP

wwPDB Information

Atom count

37 (23 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DG

Defined at

2001-12-05

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



TGP : 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 S5' S S5* N N N 0 2.414 -1.188 -3.807
2 N9 N N9 N Y N 0 1.818 1.923 -0.049
3 C4 C C4 N Y N 0 1.882 2.959 0.84
4 N3 N N3 N N N 0 2.225 2.866 2.144
5 C2 C C2 N N N 0 2.203 4.026 2.765
6 N2 N N2 N N N 0 2.519 4.145 4.093
7 N1 N N1 N N N 0 1.853 5.233 2.115
8 C6 C C6 N N N 0 1.494 5.351 0.765
9 O6 O O6 N N N 0 1.191 6.394 0.2
10 C5 C C5 N Y N 0 1.528 4.07 0.114
11 N7 N N7 N Y N 0 1.247 3.767 -1.185
12 C8 C C8 N Y N 0 1.431 2.463 -1.253
13 C2' C C2* N N N 0 0.878 -0.312 0.578
14 C5' C C5* N N N 0 1.348 -1.5 -2.377
15 C4' C C4* S N N 0 2.156 -1.432 -1.088
16 O4' O O4* N N N 0 2.678 -0.093 -0.958
17 C1' C C1* R N N 0 2.101 0.516 0.211
18 C3' C C3* S N N 0 1.309 -1.697 0.152
19 O3' O O3* N N N 0 2.127 -2.25 1.18
20 OP3 O O3P N N Y 0 1.978 -0.92 -6.807
21 P P P N N N 0 1.149 -1.32 -5.471
22 OP1 O O1P N N N 0 0.511 -2.68 -5.568
23 OP2 O O2P N N N 0 0.058 -0.121 -5.397
24 H21 H 1H2 N N N 0 1.954 4.733 4.661
25 H22 H 2H2 N N N 0 3.302 3.639 4.438
26 H1 H H1 N N N 0 1.862 6.083 2.672
27 H8 H H8 N N N 0 1.302 1.855 -2.139
28 H2' H 1H2* N N N 0 0.0080 0.0080 -0.0090
29 H2'' H 2H2* N N N 0 0.635 -0.225 1.641
30 H5' H 1H5* N N N 0 0.551 -0.755 -2.357
31 H5'' H 2H5* N N N 0 0.894 -2.488 -2.48
32 H4' H H4* N N N 0 3.008 -2.117 -1.157
33 H1' H H1* N N N 0 2.853 0.503 1.007
34 H3' H H3* N N N 0 0.475 -2.383 -0.018
35 HO3' H H3T N N Y 0 2.928 -1.706 1.218
36 HOP3 H 3HOP N N N 0 1.551 -1.044 -7.682
37 HOP2 H 2HOP N N N 0 -0.679 -0.114 -6.044



TGP : 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 S5' C5' S C sing 1.81 N N
2 S5' P S P sing 2.09 N N
3 N9 C4 N C sing 1.37 N Y
4 N9 C8 N C sing 1.38 N Y
5 N9 C1' N C sing 1.46 N N
6 C4 N3 C N sing 1.35 N N
7 C4 C5 C C doub 1.37 N Y
8 N3 C2 N C doub 1.32 N N
9 C2 N2 C N sing 1.37 N N
10 C2 N1 C N sing 1.41 N N
11 N2 H21 N H sing 0.99 N N
12 N2 H22 N H sing 0.99 N N
13 N1 C6 N C sing 1.4 N N
14 N1 H1 N H sing 1.02 N N
15 C6 O6 C O doub 1.22 N N
16 C6 C5 C C sing 1.44 N N
17 C5 N7 C N sing 1.36 N Y
18 N7 C8 N C doub 1.32 N Y
19 C8 H8 C H sing 1.08 N N
20 C2' C1' C C sing 1.52 N N
21 C2' C3' C C sing 1.51 N N
22 C2' H2' C H sing 1.1 N N
23 C2' H2'' C H sing 1.09 N N
24 C5' C4' C C sing 1.52 N N
25 C5' H5' C H sing 1.09 N N
26 C5' H5'' C H sing 1.09 N N
27 C4' O4' C O sing 1.44 N N
28 C4' C3' C C sing 1.52 N N
29 C4' H4' C H sing 1.1 N N
30 O4' C1' O C sing 1.44 N N
31 C1' H1' C H sing 1.1 N N
32 C3' O3' C O sing 1.43 N N
33 C3' H3' C H sing 1.09 N N
34 O3' HO3' O H sing 0.97 N N
35 OP3 P O P sing 1.62 N N
36 OP3 HOP3 O H sing 0.98 N N
37 P OP1 P O doub 1.51 N N
38 P OP2 P O sing 1.62 N N
39 OP2 HOP2 O H sing 0.98 N N



TGP : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
TGP 1k4t Open in New Window Polymer component 1 1
TGP 1sc7 Open in New Window Polymer component 1 1
TGP 1seu Open in New Window Polymer component 1 1
TGP 1t8i Open in New Window Polymer component 1 1