Structure of PDB 3upq Chain A Binding Site BS04

Receptor Information
>3upq Chain A (length=308) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACS
IPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQM
WYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQK
AAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSL
RQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYF
TGSAHFNRSMRALAKTKGMSLSEHALSTAVGRVLPTPTEKDVFRLLGLPY
REPAERDW
Ligand information
Ligand IDZAN
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-29(19,20)15-30(21,22)28-31(23,24)25/h2-4,6-7,10,17-18H,1H2,(H2,11,12,13)(H2,23,24,25)(H3,15,19,20,21,22)/t4-,6-,7-,10-/m1/s1
InChIKeyWUPFAKUEHUVIDK-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O)N
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H17 N6 O12 P3
Name5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
ChEMBL
DrugBank
ZINCZINC000034177510
PDB chain3upq Chain A Residue 0 [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]
PDB3upq The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda
Resolution1.95 Å
Binding residue
(original residue number in PDB)		R386 G416 S417 R420 C425 G426 D427 D429 Y505 F506 T507 G508 N513
Binding residue
(residue number reindexed from 1)		R135 G165 S166 R169 C174 G175 D176 D178 Y249 F250 T251 G252 N257
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D427 D429 D490
Catalytic site (residue number reindexed from 1) D176 D178 D234
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:3upq, PDBe:3upq, PDBj:3upq
PDBsum3upq
PubMed22584622
UniProtQ9UGP5|DPOLL_HUMAN DNA polymerase lambda (Gene Name=POLL)

[Back to BioLiP]