Structure of PDB 2cvv Chain A Binding Site BS01

Receptor Information
>2cvv Chain A (length=651) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYD
RDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALE
TYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKEC
ALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQ
GGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLF
MKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKL
WYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPD
ETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRN
YYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFET
IYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTL
RKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMYSFQVVNPYL
LRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTI
INMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRT
Q
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain2cvv Chain A Residue 1001 [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]
PDB2cvv Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation
Resolution2.9 Å
Binding residue
(original residue number in PDB)		D226 S227 I228 R256 I262 A263
Binding residue
(residue number reindexed from 1)		D138 S139 I140 R168 I174 A175
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) C218 N426 C428 E430 C443 Y741 Y742
Catalytic site (residue number reindexed from 1) C130 N338 C340 E342 C355 Y646 Y647
Enzyme Commision number 1.17.4.1: ribonucleoside-diphosphate reductase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016491 oxidoreductase activity
GO:0042802 identical protein binding
Biological Process
GO:0009263 deoxyribonucleotide biosynthetic process
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005971 ribonucleoside-diphosphate reductase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2cvv, PDBe:2cvv, PDBj:2cvv
PDBsum2cvv
PubMed16537479
UniProtP21524|RIR1_YEAST Ribonucleoside-diphosphate reductase large chain 1 (Gene Name=RNR1)

[Back to BioLiP]