Structure of PDB 2cvw Chain A Binding Site BS01

Receptor Information
>2cvw Chain A (length=649) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDRD
FQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALETY
NLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECAL
ISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQGG
NKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFMK
RVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWY
SILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDET
AVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNYY
PVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETIY
HASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLRK
DIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMYSFQVVNPYLLR
DLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIIN
MAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ
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 chain2cvw 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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PDB2cvw 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 N270
Binding residue
(residue number reindexed from 1)		D136 S137 I138 I141 R166 I172 A173 N180
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 N336 C338 E340 C353 Y644 Y645
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:2cvw, PDBe:2cvw, PDBj:2cvw
PDBsum2cvw
PubMed16537479
UniProtP21524|RIR1_YEAST Ribonucleoside-diphosphate reductase large chain 1 (Gene Name=RNR1)

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