BioLiP

Receptor Information

>1zmd Chain D (length=472) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

QPIDADVTVIGSGPGGYVAAIKAAQLGFKTVCIEKNETLGGTCLNVGCIP
SKALLNNSHYYHMAHGTDFASRGIEMSEVRLNLDKMMEQKSTAVKALTGG
IAHLFKQNKVVHVNGYGKITGKNQVTATKADGGTQVIDTKNILIATGSEV
TPFPGITIDEDTIVSSTGALSLKKVPEKMVVIGAGVIGVELGSVWQRLGA
DVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKVTGATKKSDG
KIDVSIEAASGGKAEVITCDVLLVCIGRRPFTKNLGLEELGIELDPRGRI
PVNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEGIICVEGMAGGAVHIDYN
CVPSVIYTHPEVAWVGKSEEQLKEEGIEYKVGKFPFAANSRAKTNADTDG
MVKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASCEDIARVCHAH
PTLSEAFREANLAASFGKSINF

Ligand ID

NAI

InChI

InChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1

InChIKey

BOPGDPNILDQYTO-NNYOXOHSSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341	NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)O)N
CACTVS 3.341	NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O

Formula

C21 H29 N7 O14 P2

Name

1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE;
NADH

PDB chain

1zmd Chain D Residue 481 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	1zmd Crystal Structure of Human Dihydrolipoamide Dehydrogenase: NAD+/NADH Binding and the Structural Basis of Disease-causing Mutations
Resolution	2.08 Å
Binding residue (original residue number in PDB)	G185 V188 I189 E192 E208 F209 L210 I278 G279 M326 L327 V357 Y359
Binding residue (residue number reindexed from 1)	G183 V186 I187 E190 E206 F207 L208 I276 G277 M324 L325 V355 Y357
Annotation score	4

Catalytic site (original residue number in PDB)	L41 C45 C50 S53 V188 E192 H450 H452 E457
Catalytic site (residue number reindexed from 1)	L39 C43 C48 S51 V186 E190 H448 H450 E455
Enzyme Commision number	1.8.1.4: dihydrolipoyl dehydrogenase.

	Molecular Function
GO:0004148	dihydrolipoyl dehydrogenase activity
GO:0005515	protein binding
GO:0016491	oxidoreductase activity
GO:0016668	oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor
GO:0034604	pyruvate dehydrogenase (NAD+) activity
GO:0047101	branched-chain alpha-keto acid dehydrogenase activity
GO:0050660	flavin adenine dinucleotide binding

	Biological Process
GO:0006086	acetyl-CoA biosynthetic process from pyruvate
GO:0006120	mitochondrial electron transport, NADH to ubiquinone
GO:0006508	proteolysis
GO:0007369	gastrulation
GO:0009083	branched-chain amino acid catabolic process
GO:0042391	regulation of membrane potential
GO:0048240	sperm capacitation

	Cellular Component
GO:0001669	acrosomal vesicle
GO:0005634	nucleus
GO:0005739	mitochondrion
GO:0005759	mitochondrial matrix
GO:0005929	cilium
GO:0031410	cytoplasmic vesicle
GO:0031514	motile cilium
GO:0043159	acrosomal matrix
GO:0045252	oxoglutarate dehydrogenase complex
GO:0045254	pyruvate dehydrogenase complex
GO:0160157	branched-chain alpha-ketoacid dehydrogenase complex
GO:0160167	oxoadipate dehydrogenase complex
GO:1902493	acetyltransferase complex

PDB	RCSB:1zmd, PDBe:1zmd, PDBj:1zmd
PDBsum	1zmd
PubMed	15946682
UniProt	P09622\|DLDH_HUMAN Dihydrolipoyl dehydrogenase, mitochondrial (Gene Name=DLD)

[Back to BioLiP]

Structure of PDB 1zmd Chain D Binding Site BS02