Structure of PDB 2f5z Chain D Binding Site BS01

Receptor Information
>2f5z Chain D (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 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 chain2f5z Chain D 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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PDB2f5z Structural Insight into Interactions between Dihydrolipoamide Dehydrogenase (E3) and E3 Binding Protein of Human Pyruvate Dehydrogenase Complex.
Resolution2.18 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 R280 F283 G319 D320 M326 L327 A328 H329
Binding residue
(residue number reindexed from 1)		I9 G10 G12 P13 G14 E33 K34 N35 G40 T41 C42 G46 C47 K51 Y115 G116 A144 T145 G146 S165 I186 R277 F280 G316 D317 M323 L324 A325 H326
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) 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

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2f5z, PDBe:2f5z, PDBj:2f5z
PDBsum2f5z
PubMed16442803
UniProtP09622|DLDH_HUMAN Dihydrolipoyl dehydrogenase, mitochondrial (Gene Name=DLD)

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