Structure of PDB 2cvy Chain A Binding Site BS02

Receptor Information
>2cvy Chain A (length=640) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDRD
FQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETY
NLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECAL
ISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVAFAL
YLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMKRVEENGTWT
LFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEAQTET
GTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDETAVCNLASVA
LPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSN
MRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETIYHASMEASCE
LAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLRKDIMKHGVRN
SLTMAPMPTASTSQILGYNECFEPVTSNMYSFQVVNPYLLRDLVDLGIWD
EGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINMAADRSVYI
DQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ
Ligand information
Ligand IDTTP
InChIInChI=1S/C10H17N2O14P3/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,21,22)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyNHVNXKFIZYSCEB-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H17 N2 O14 P3
NameTHYMIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL363559
DrugBankDB02452
ZINCZINC000008215959
PDB chain2cvy 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

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PDB2cvy Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation
Resolution2.4 Å
Binding residue
(original residue number in PDB)		D226 S227 I228 I231 R256 I262 A263
Binding residue
(residue number reindexed from 1)		D136 S137 I138 I141 R166 I172 A173
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) C128 N327 C329 E331 C344 Y635 Y636
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:2cvy, PDBe:2cvy, PDBj:2cvy
PDBsum2cvy
PubMed16537479
UniProtP21524|RIR1_YEAST Ribonucleoside-diphosphate reductase large chain 1 (Gene Name=RNR1)

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