Structure of PDB 5nhg Chain D Binding Site BS01

Receptor Information
>5nhg 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
SKALLNNSHYYHMAHGKDFASRGIEMSEVRLNLDKMMEQKSTAVKALTGG
IAHLFKQNKVVHVNGYGKITGKNQVTATKADGGTQVIDTKNILIATGSEV
TPFPGITIDEDTIVSSTGALSLKKVPEKMVVIGAGVIGVELGSVWQRLGA
DVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKVTGATKKSDG
KIDVSIEAASGGKAEVITCDVLLVCIGRRPFTKNLGLEELGIELDPRGRI
PVNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEGIICVEGMAGGAVHIDYN
CVPSVIYTHPEVAWVGKSEEQLKEEGIEYKVGKFPFAANSRAKTNADTDG
MVKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASCEDIARVCHAH
PTLSEAFREANLAASFGKSINF
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 chain5nhg Chain D Residue 500 [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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PDB5nhg Crystal structures of the disease-causing D444V mutant and the relevant wild type human dihydrolipoamide dehydrogenase.
Resolution2.27 Å
Binding residue
(original residue number in PDB)		I12 G13 G15 P16 E36 K37 N38 G43 T44 C45 G49 C50 K54 Y118 G119 T148 G149 S168 I189 R280 F283 G319 D320 M326 L327 A328 H329 A331
Binding residue
(residue number reindexed from 1)		I10 G11 G13 P14 E34 K35 N36 G41 T42 C43 G47 C48 K52 Y116 G117 T146 G147 S166 I187 R278 F281 G317 D318 M324 L325 A326 H327 A329
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C45 C50 S53 V188 E192 H452 E457
Catalytic site (residue number reindexed from 1) C43 C48 S51 V186 E190 H450 E455
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:5nhg, PDBe:5nhg, PDBj:5nhg
PDBsum5nhg
PubMed29908278
UniProtP09622|DLDH_HUMAN Dihydrolipoyl dehydrogenase, mitochondrial (Gene Name=DLD)

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