Structure of PDB 3s8c Chain A Binding Site BS02

Receptor Information
>3s8c Chain A (length=666) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YATLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNI
VMENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMR
VALGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAM
KEDSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLI
PMIRVFNNTARYVDQGGNKAPGAFALYLEPWHADIFDFIDIRKNHGKEEI
RARDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTR
YEKEGRGKTIKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIK
SSNLCCEIVEYSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEI
AKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPF
DSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFD
MWDQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEP
VTSNMYSFQVVNPYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQEL
KDLYKTVWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFY
GWKKGLKTGMYYLRTQ
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 chain3s8c Chain A Residue 891 [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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PDB3s8c Structural and biochemical basis of lethal mutant R293A of yeast ribonucleotide reductase
Resolution2.77 Å
Binding residue
(original residue number in PDB)		A201 S202 S217 G246 G247 K292 P607 T608 A609 S610 T611
Binding residue
(residue number reindexed from 1)		A128 S129 S144 G173 G174 K219 P534 T535 A536 S537 T538
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) C145 N353 C355 E357 C370 Y661 Y662
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3s8c, PDBe:3s8c, PDBj:3s8c
PDBsum3s8c
PubMed
UniProtP21524|RIR1_YEAST Ribonucleoside-diphosphate reductase large chain 1 (Gene Name=RNR1)

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