Structure of PDB 1zmd Chain E Binding Site BS01

Receptor Information
>1zmd Chain E (length=473) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DQPIDADVTVIGSGPGGYVAAIKAAQLGFKTVCIEKNETLGGTCLNVGCI
PSKALLNNSHYYHMAHGTDFASRGIEMSEVRLNLDKMMEQKSTAVKALTG
GIAHLFKQNKVVHVNGYGKITGKNQVTATKADGGTQVIDTKNILIATGSE
VTPFPGITIDEDTIVSSTGALSLKKVPEKMVVIGAGVIGVELGSVWQRLG
ADVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKVTGATKKSD
GKIDVSIEAASGGKAEVITCDVLLVCIGRRPFTKNLGLEELGIELDPRGR
IPVNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEGIICVEGMAGGAVHIDY
NCVPSVIYTHPEVAWVGKSEEQLKEEGIEYKVGKFPFAANSRAKTNADTD
GMVKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASCEDIARVCHA
HPTLSEAFREANLAASFGKSINF
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain1zmd Chain E Residue 480 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1zmd Crystal Structure of Human Dihydrolipoamide Dehydrogenase: NAD+/NADH Binding and the Structural Basis of Disease-causing Mutations
Resolution2.08 Å
Binding residue
(original residue number in PDB)		I12 G13 G15 P16 G17 E36 K37 N38 G43 T44 C45 G49 C50 K54 Y118 G119 A147 T148 G149 S168 I189 F283 D320 M326 L327 A328 H329
Binding residue
(residue number reindexed from 1)		I11 G12 G14 P15 G16 E35 K36 N37 G42 T43 C44 G48 C49 K53 Y117 G118 A146 T147 G148 S167 I188 F282 D319 M325 L326 A327 H328
Annotation score2
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) L40 C44 C49 S52 V187 E191 H449 H451 E456
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

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1zmd, PDBe:1zmd, PDBj:1zmd
PDBsum1zmd
PubMed15946682
UniProtP09622|DLDH_HUMAN Dihydrolipoyl dehydrogenase, mitochondrial (Gene Name=DLD)

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