BioLiP

Receptor Information

>1zmd Chain F (length=471) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

PIDADVTVIGSGPGGYVAAIKAAQLGFKTVCIEKNETLGGTCLNVGCIPS
KALLNNSHYYHMAHGTDFASRGIEMSEVRLNLDKMMEQKSTAVKALTGGI
AHLFKQNKVVHVNGYGKITGKNQVTATKADGGTQVIDTKNILIATGSEVT
PFPGITIDEDTIVSSTGALSLKKVPEKMVVIGAGVIGVELGSVWQRLGAD
VTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKVTGATKKSDGK
IDVSIEAASGGKAEVITCDVLLVCIGRRPFTKNLGLEELGIELDPRGRIP
VNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEGIICVEGMAGGAVHIDYNC
VPSVIYTHPEVAWVGKSEEQLKEEGIEYKVGKFPFAANSRAKTNADTDGM
VKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASCEDIARVCHAHP
TLSEAFREANLAASFGKSINF

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 F Residue 481 [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	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 G187 V188 I189 E192 E208 F209 I278 G279 R280 M326 L327 V357 Y359
Binding residue (residue number reindexed from 1)	G182 G184 V185 I186 E189 E205 F206 I275 G276 R277 M323 L324 V354 Y356
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)	L38 C42 C47 S50 V185 E189 H447 H449 E454
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)

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Structure of PDB 1zmd Chain F Binding Site BS02