Structure of PDB 3mi2 Chain A Binding Site BS01

Receptor Information
>3mi2 Chain A (length=257) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KELSFGARAELPRIHPVASKLLRLMQKKETNLCLSADVSLARELLQLADA
LGPSICMLKTHVDILNDFTLDVMKELITLAKCHEFLIFEDRKFADIGNTV
KKQYEGGIFKIASWADLVNAHVVPGSGVVKGLQEVGLPLHRGCLLIAEMS
STGSLATGDYTRAAVRMAEEHSEFVVGFISGSRVSMKPEFLHLTPGVQLE
AGGDNLGQQYNSPQEVIGKRGSDIIIVGRGIISAADRLEAAEMYRKAAWE
AYLSRLG
Ligand information
Ligand IDPFU
InChIInChI=1S/C9H14N3O9P/c10-9(16)4-6(14)3(11-12-4)8-7(15)5(13)2(21-8)1-20-22(17,18)19/h2,5,7-8,13-15H,1H2,(H2,10,16)(H,11,12)(H2,17,18,19)/t2-,5-,7-,8+/m1/s1
InChIKeyCUHDHRMGDRLFLH-FLLFQEBCSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C(C1C(C(C(O1)c2c(c([nH]n2)C(=O)N)O)O)O)OP(=O)(O)O
OpenEye OEToolkits 1.7.0C([C@@H]1[C@H]([C@H]([C@@H](O1)c2c(c([nH]n2)C(=O)N)O)O)O)OP(=O)(O)O
CACTVS 3.370NC(=O)c1[nH]nc([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)c1O
CACTVS 3.370NC(=O)c1[nH]nc([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)c1O
ACDLabs 12.01O=C(N)c1c(O)c(nn1)C2OC(COP(=O)(O)O)C(O)C2O
FormulaC9 H14 N3 O9 P
Name(1S)-1,4-anhydro-1-(5-carbamoyl-4-hydroxy-1H-pyrazol-3-yl)-5-O-phosphono-D-ribitol;
Pyrazofurin Monophosphate
ChEMBLCHEMBL1164953
DrugBank
ZINCZINC000049803241
PDB chain3mi2 Chain A Residue 1 [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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PDB3mi2 Structural determinants for the inhibitory ligands of orotidine-5'-monophosphate decarboxylase.
Resolution1.2 Å
Binding residue
(original residue number in PDB)		S68 D70 K92 H94 K125 M182 S183 P228 Q241 Y243 G261 R262
Binding residue
(residue number reindexed from 1)		S35 D37 K59 H61 K92 M149 S150 P195 Q208 Y210 G228 R229
Annotation score1
Binding affinityMOAD: Ki=0.00000079M
PDBbind-CN: -logKd/Ki=7.77,Ki=17nM
BindingDB: Ki=17nM
Enzymatic activity
Enzyme Commision number 2.4.2.10: orotate phosphoribosyltransferase.
4.1.1.23: orotidine-5'-phosphate decarboxylase.
Gene Ontology
Molecular Function
GO:0004590 orotidine-5'-phosphate decarboxylase activity
Biological Process
GO:0006207 'de novo' pyrimidine nucleobase biosynthetic process
GO:0044205 'de novo' UMP biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3mi2, PDBe:3mi2, PDBj:3mi2
PDBsum3mi2
PubMed20452222
UniProtP11172|UMPS_HUMAN Uridine 5'-monophosphate synthase (Gene Name=UMPS)

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