Structure of PDB 2eud Chain A Binding Site BS01

Receptor Information
>2eud Chain A (length=648) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVMENKDKLNSAIVYDR
DFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVALGIHGRDIEAALET
YNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKEDSIEGIYDTLKECA
LISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPMIRVFNNTARYVDQG
GNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALWIPDLFM
KRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLW
YSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVEYSAPDE
TAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNRVIDRNY
YPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNIQIFETI
YHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMWDWDTLR
KDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMFQVVNPYLLRD
LVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQKTIINM
AADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYYLRTQ
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain2eud Chain A Residue 890 [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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PDB2eud Structures of eukaryotic ribonucleotide reductase I define gemcitabine diphosphate binding and subunit assembly.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D226 S227 I228 I231 R256 I262 A263
Binding residue
(residue number reindexed from 1)		D137 S138 I139 I142 R167 I173 A174
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) C129 N337 C339 E341 C354 Y643 Y644
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:2eud, PDBe:2eud, PDBj:2eud
PDBsum2eud
PubMed16537480
UniProtP21524|RIR1_YEAST Ribonucleoside-diphosphate reductase large chain 1 (Gene Name=RNR1)

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