Structure of PDB 2cvx Chain A Binding Site BS02

Receptor Information
>2cvx Chain A (length=664) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVM
ENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVA
LGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKE
DSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPM
IRVFNNTARYVDQGGNKRPGAFALYLEPWHADIFDFIDIRKNHGKEEIRA
RDLFPALWIPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYE
KEGRGKTIKAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSS
NLCCEIVEYSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAK
VVTRNLNRVIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDS
EEARLLNIQIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMW
DQKPYGMWDWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVT
SNMYSFQVVNPYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKD
LYKTVWEISQKTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGW
KKGLKTGMYYLRTQ
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain2cvx Chain A Residue 1002 [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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PDB2cvx Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation
Resolution2.2 Å
Binding residue
(original residue number in PDB)		A201 S202 S217 C218 G246 G247 Q288 R293 A296 L427 C428 E430 L445 T608 A609 S610 T611
Binding residue
(residue number reindexed from 1)		A126 S127 S142 C143 G171 G172 Q213 R218 A221 L352 C353 E355 L370 T533 A534 S535 T536
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) C143 N351 C353 E355 C368 Y659 Y660
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2cvx, PDBe:2cvx, PDBj:2cvx
PDBsum2cvx
PubMed16537479
UniProtP21524|RIR1_YEAST Ribonucleoside-diphosphate reductase large chain 1 (Gene Name=RNR1)

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