Structure of PDB 5j5z Chain B Binding Site BS01

Receptor Information
>5j5z Chain B (length=482) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVLFQGPGADQPIDADVTVIGSGPGGYVAAIKAAQLGFKTVCIEKNETLG
GTCLNVGCIPSKALLNNSHYYHMAHGKDFASRGIEMSEVRLNLDKMMEQK
STAVKALTGGIAHLFKQNKVVHVNGYGKITGKNQVTATKADGGTQVIDTK
NILIATGSEVTPFPGITIDEDTIVSSTGALSLKKVPEKMVVIGAGVIGVE
LGSVWQRLGADVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTK
VTGATKKSDGKIDVSIEAASGGKAEVITCDVLLVCIGRRPFTKNLGLEEL
GIELDPRGRIPVNTRFQTKIPNIYAIGDVVAGPMLAHKAEDEGIICVEGM
AGGAVHIDYNCVPSVIYTHPEVAWVGKSEEQLKEEGIEYKVGKFPFAANS
RAKTNADTDGMVKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASC
EVIARVCHAHPTLSEAFREANLAASFGKSINF
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 chain5j5z Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5j5z Crystal structures of the disease-causing D444V mutant and the relevant wild type human dihydrolipoamide dehydrogenase.
Resolution1.84 Å
Binding residue
(original residue number in PDB)		I12 G13 G15 P16 G17 E36 K37 N38 G43 T44 C45 G49 C50 K54 Y118 G119 T148 G149 S168 I189 R280 F283 G319 D320 L327 A328 H329
Binding residue
(residue number reindexed from 1)		I20 G21 G23 P24 G25 E44 K45 N46 G51 T52 C53 G57 C58 K62 Y126 G127 T156 G157 S176 I197 R288 F291 G327 D328 L335 A336 H337
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) L49 C53 C58 S61 V196 E200 H458 H460 E465
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5j5z, PDBe:5j5z, PDBj:5j5z
PDBsum5j5z
PubMed29908278
UniProtP09622|DLDH_HUMAN Dihydrolipoyl dehydrogenase, mitochondrial (Gene Name=DLD)

[Back to BioLiP]