Structure of PDB 3pmn Chain A Binding Site BS04

Receptor Information
>3pmn Chain A (length=312) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQE
ACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKT
AQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQT
VQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLL
DSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACAL
LYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVPGRVLPTPTEKDVFRLL
GLPYREPAERDW
Ligand information
Ligand ID1GC
InChIInChI=1S/C11H18N5O12P3/c12-11-14-9-8(10(18)15-11)13-3-16(9)7-1-5(17)6(27-7)2-26-29(19,20)4-30(21,22)28-31(23,24)25/h3,5-7,17H,1-2,4H2,(H,19,20)(H,21,22)(H2,23,24,25)(H3,12,14,15,18)/t5-,6+,7+/m0/s1
InChIKeyJTBKCZGNQPBEJY-RRKCRQDMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc2c(n1C3CC(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.7.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O3
CACTVS 3.370NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)O3
FormulaC11 H18 N5 O12 P3
Name2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine
ChEMBLCHEMBL1162300
DrugBank
ZINCZINC000040953629
PDB chain3pmn Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3pmn Replication infidelity via a mismatch with Watson-Crick geometry.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R386 S417 R420 G426 D427 D429 Y505 F506 T507 G508 A510 N513 R517
Binding residue
(residue number reindexed from 1)		R138 S169 R172 G178 D179 D181 Y252 F253 T254 G255 A257 N260 R264
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D427 D429 D490
Catalytic site (residue number reindexed from 1) D179 D181 D237
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
4.2.99.-
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0016779 nucleotidyltransferase activity
GO:0034061 DNA polymerase activity
Biological Process
GO:0006281 DNA repair

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3pmn, PDBe:3pmn, PDBj:3pmn
PDBsum3pmn
PubMed21233421
UniProtQ9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)

[Back to BioLiP]