Structure of PDB 6cer Chain C Binding Site BS01

Receptor Information

>6cer Chain C (length=328) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ANDATFEIKKCDLHRLEEGPPVTTVLTREDGLKYYRMMQTVRRMELKADQ
LYKQKIIRGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLS
VREILAELTGRKGGCAKGKGGSMHMYAKNFYGGNGIMGAQVPLGAGIALA
CKYNGKDEVCLTLYGDGAANQGQIFEAYNMAALWKLPCIFICENNRAAAS
TDYYKRGDFIPGLRVDGMDILCVREATRFAAAYCRSGKGPILMELQTVRS
KSDPIMLLKDRMVNSNLASVEELKEIDVEVRKEIEDAAQFATADPEPPLE
ELGYHIYSSDPPFEVRGANQWIKFKSVS

Ligand information

Ligand ID

TPP

InChI

InChI=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

InChIKey

AYEKOFBPNLCAJY-UHFFFAOYSA-O

SMILES

Software	SMILES
CACTVS 3.341	Cc1ncc(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
OpenEye OEToolkits 1.5.0	Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCO[P@](=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0	Cc1c(sc[n+]1Cc2cnc(nc2N)C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341	Cc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OCCc1sc[n+](c1C)Cc2c(nc(nc2)C)N

Formula

C12 H19 N4 O7 P2 S

Name

THIAMINE DIPHOSPHATE

PDB chain

6cer Chain C Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	6cer Pyruvate dehydrogenase complex deficiency is linked to regulatory loop disorder in the alpha V138M variant of human pyruvate dehydrogenase.
Resolution	2.69 Å
Binding residue (original residue number in PDB)	Y89 R90 M138
Binding residue (residue number reindexed from 1)	Y88 R89 M137
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	Q51 G136
Catalytic site (residue number reindexed from 1)	Q50 G135
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:6cer, PDBe:6cer, PDBj:6cer
PDBsum	6cer
PubMed	29970614
UniProt	P08559\|ODPA_HUMAN Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial (Gene Name=PDHA1)

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