Structure of PDB 2cvu Chain A Binding Site BS02

Receptor Information
>2cvu 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 IDCDP
InChIInChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyZWIADYZPOWUWEW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
FormulaC9 H15 N3 O11 P2
NameCYTIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL425252
DrugBankDB04555
ZINCZINC000008215624
PDB chain2cvu Chain A Residue 1002 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2cvu Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation
Resolution2.9 Å
Binding residue
(original residue number in PDB)		A201 S202 S217 C218 G247 L427 C428 E430 M606 P607 T608 A609 T611
Binding residue
(residue number reindexed from 1)		A113 S114 S129 C130 G159 L339 C340 E342 M518 P519 T520 A521 T523
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:2cvu, PDBe:2cvu, PDBj:2cvu
PDBsum2cvu
PubMed16537479
UniProtP21524|RIR1_YEAST Ribonucleoside-diphosphate reductase large chain 1 (Gene Name=RNR1)

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