Structure of PDB 1zmc Chain F Binding Site BS02

Receptor Information

>1zmc Chain F (length=471) Species: 9606 (Homo sapiens)

PIDADVTVIGSGPGGYVAAIKAAQLGFKTVCIEKNETLGGTCLNVGCIPS
KALLNNSHYYHMAHGTDFASRGIEMSEVRLNLDKMMEQKSTAVKALTGGI
AHLFKQNKVVHVNGYGKITGKNQVTATKADGGTQVIDTKNILIATGSEVT
PFPGITIDEDTIVSSTGALSLKKVPEKMVVIGAGVIGVELGSVWQRLGAD
VTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKVTGATKKSDGK
IDVSIEAASGGKAEVITCDVLLVCIGRRPFTKNLGLEELGIELDPRGRIP
VNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEGIICVEGMAGGAVHIDYNC
VPSVIYTHPEVAWVGKSEEQLKEEGIEYKVGKFPFAANSRAKTNADTDGM
VKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASCEDIARVCHAHP
TLSEAFREANLAASFGKSINF

Ligand information

• Ligand ID: NAD
• InChI: InChI=1S/C21H27N7O14P2/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/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
• InChIKey: BAWFJGJZGIEFAR-NNYOXOHSSA-N
• SMILES:
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[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: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
  CACTVS 3.341: NC(=O)c1ccc[n+](c1)[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
  OpenEye OEToolkits 1.5.0: c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
• Formula: C21 H27 N7 O14 P2
• Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
• ChEMBL: CHEMBL1234613
• DrugBank: DB14128
• PDB chain: 1zmc Chain F Residue 481

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1zmc Crystal Structure of Human Dihydrolipoamide Dehydrogenase: NAD(+)/NADH Binding and the Structural Basis of Disease-causing Mutations
• Resolution: 2.53 Å
• Binding residue (original residue number in PDB): I184 G185 E208 F209 L210 G215 V216 V243 I278 G279
• Binding residue (residue number reindexed from 1): I181 G182 E205 F206 L207 G212 V213 V240 I275 G276
• Annotation score: 4

Enzymatic activity

• 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.

Gene Ontology

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

External links

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