Chemical Components in the PDB

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D3 : Summary

Code

D3

One-letter code

N

Molecule name

1-(2-DEOXY-BETA-D-RIBOFURANOSYL)-4-(3-BENZAMIDO)PHENYLIMIDAZOLE

Systematic names

ProgramVersionName
ACDLabs 10.04 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-{3-[(phenylcarbonyl)amino]phenyl}-1H-imidazole
OpenEye OEToolkits 1.5.0 [(2R,3S,5R)-5-[4-(3-benzamidophenyl)imidazol-1-yl]-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C21 H22 N3 O7 P

Formal charge

0

Molecular weight

459.389 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(c1ccccc1)Nc4cccc(c2ncn(c2)C3OC(C(O)C3)COP(=O)(O)O)c4
SMILES CACTVS 3.341 O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc(c2)c3cccc(NC(=O)c4ccccc4)c3
SMILES OpenEye OEToolkits 1.5.0 c1ccc(cc1)C(=O)Nc2cccc(c2)c3cn(cn3)C4CC(C(O4)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.341 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc(c2)c3cccc(NC(=O)c4ccccc4)c3
Canonical SMILES OpenEye OEToolkits 1.5.0 c1ccc(cc1)C(=O)Nc2cccc(c2)c3cn(cn3)[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C21H22N3O7P/c25-18-10-20(31-19(18)12-30-32(27,28)29)24-11-17(22-13-24)15-7-4-8-16(9-15)23-21(26)14-5-2-1-3-6-14/h1-9,11,13,18-20,25H,10,12H2,(H,23,26)(H2,27,28,29)/t18-,19+,20+/m0/s1

IUPAC InChI key

OCVGIISTWVVLJA-XUVXKRRUSA-N
D3

wwPDB Information

Atom count

54 (32 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

HETAIN

Is modified

Yes

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned