Structure of PDB 1ni4 Chain C Binding Site BS02

Receptor Information
>1ni4 Chain C (length=362) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKYYRMMQTVRRMELKA
DQLYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRG
LSVREILAELTGRKGGCAKGKGGSMHMYAKNFYGGNGIVGAQVPLGAGIA
LACKYNGKDEVCLTLYGDGAANQGQIFEAYNMAALWKLPCIFICENNRYG
MGTSVERAAASTDYYKRGDFIPGLRVDGMDILCVREATRFAAAYCRSGKG
PILMELQTYRYHGHSMSDPGVSYRTREEIQEVRSKSDPIMLLKDRMVNSN
LASVEELKEIDVEVRKEIEDAAQFATADPEPPLEELGYHIYSSDPPFEVR
GANQWIKFKSVS
Ligand information
Ligand IDTPP
InChIInChI=1S/C12H18N4O7P2S/c1-8-11(3-4-22-25(20,21)23-24(17,18)19)26-7-16(8)6-10-5-14-9(2)15-12(10)13/h5,7H,3-4,6H2,1-2H3,(H4-,13,14,15,17,18,19,20,21)/p+1
InChIKeyAYEKOFBPNLCAJY-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N
FormulaC12 H19 N4 O7 P2 S
NameTHIAMINE DIPHOSPHATE
ChEMBLCHEMBL1236376
DrugBank
ZINCZINC000008215517
PDB chain1ni4 Chain C Residue 1330 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1ni4 Structural Basis for Flip-Flop Action of Thiamin Pyrophosphate-Dependent Enzymes Revealed by Human Pyruvate Dehydrogenase
Resolution1.95 Å
Binding residue
(original residue number in PDB)		Y89 R90 V138 G166 D167 G168 A169 N196 Y198 G199 H263
Binding residue
(residue number reindexed from 1)		Y90 R91 V139 G167 D168 G169 A170 N197 Y199 G200 H264
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q51 G136 R259 H263 S264 Y272
Catalytic site (residue number reindexed from 1) Q52 G137 R260 H264 S265 Y273
Enzyme Commision number 1.2.4.1: pyruvate dehydrogenase (acetyl-transferring).
Gene Ontology
Molecular Function
GO:0004738 pyruvate dehydrogenase activity
GO:0004739 pyruvate dehydrogenase (acetyl-transferring) activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0016624 oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
GO:0034604 pyruvate dehydrogenase (NAD+) activity
GO:0046872 metal ion binding
Biological Process
GO:0006006 glucose metabolic process
GO:0006086 acetyl-CoA biosynthetic process from pyruvate
GO:0006090 pyruvate metabolic process
GO:0006099 tricarboxylic acid cycle
Cellular Component
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0043231 intracellular membrane-bounded organelle
GO:0045254 pyruvate dehydrogenase complex
GO:1902494 catalytic complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1ni4, PDBe:1ni4, PDBj:1ni4
PDBsum1ni4
PubMed12651851
UniProtP08559|ODPA_HUMAN Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (Gene Name=PDHA1)

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