Structure of PDB 3rsr Chain A Binding Site BS01

Receptor Information
>3rsr Chain A (length=610) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYD
RDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALE
TYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKEC
ALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVFA
LYLEPWHADIFDFIDIRKDLFPALWIPDLFMKRVEENGTWTLFSPTSAPG
LSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEAQTETGTPFVVYKD
ACNRKSNQKNLGVIKSSNLCCEIVEYSAPDETAVCNLASVALPAFIETSK
TSTYNFKKLHEIAKVVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQG
LADTFMLLRLPFDSEEARLLNIQIFETIYHASMEASCELAQKDGPYETFQ
GSPASQGILQFDMWDQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTTSQ
ILGYNECFEPNPYLLRDLVDLGIWQYLITQNGSIQGLPNVPQELKDLYKT
VWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGL
KTGMYYLRTQ
Ligand information
Ligand IDN5P
InChIInChI=1S/C13H17N2O14P3/c16-11-6-13(14-4-3-8-5-9(15(17)18)1-2-10(8)14)27-12(11)7-26-31(22,23)29-32(24,25)28-30(19,20)21/h1-5,11-13,16H,6-7H2,(H,22,23)(H,24,25)(H2,19,20,21)/t11-,12+,13+/m0/s1
InChIKeyJJJBDAFRCKSXDR-YNEHKIRRSA-N
SMILES
SoftwareSMILES
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O
OpenEye OEToolkits 1.7.2c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)cc1[N+](=O)[O-]
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O
ACDLabs 12.01[O-][N+](=O)c2cc1ccn(c1cc2)C3OC(C(O)C3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O
FormulaC13 H17 N2 O14 P3
Name1-{2-DEOXY-5-O-[(R)-HYDROXY{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}PHOSPHORYL]-BETA-D-ERYTHRO-PENTOFURANOSYL}-5-NITRO -1H-INDOLE;
5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-TRIPHOSPHATE
ChEMBL
DrugBank
ZINCZINC000059142887
PDB chain3rsr Chain A Residue 841 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3rsr Evaluating the therapeutic potential of a non-natural nucleotide that inhibits human ribonucleotide reductase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D226 S227 I228 R256 I262 A263 G264 T265
Binding residue
(residue number reindexed from 1)		D138 S139 I140 R168 I174 A175 G176 T177
Annotation score1
Binding affinityMOAD: Kd=44uM
PDBbind-CN: -logKd/Ki=4.36,Kd=44uM
Enzymatic activity
Catalytic site (original residue number in PDB) C218 N406 C408 E410 C423 Y693 Y694
Catalytic site (residue number reindexed from 1) C130 N318 C320 E322 C335 Y605 Y606
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:3rsr, PDBe:3rsr, PDBj:3rsr
PDBsum3rsr
PubMed22933704
UniProtP21524|RIR1_YEAST Ribonucleoside-diphosphate reductase large chain 1 (Gene Name=RNR1)

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