Structure of PDB 1ivh Chain B Binding Site BS01

Receptor Information
>1ivh Chain B (length=387) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VDDAINGLSEEQRQLRQTMAKFLQEHLAPKAQEIDRSNEFKNLREFWKQL
GNLGVLGITAPVQYGGSGLGYLEHVLVMEEISRASGAVGLSYGAHSNLCI
NQLVRNGNEAQKEKYLPKLISGEYIGALAMSEPNAGSDVVSMKLKAEKKG
NHYILNGNKFWITNGPDADVLIVYAKTDLAAVPASRGITAFIVEKGMPGF
STSKKLDKLGMRGSNTCELIFEDCKIPAANILGHENKGVYVLMSGLDLER
LVLAGGPLGLMQAVLDHTIPYLHVREAFGQKIGHFQLMQGKMADMYTRLM
ACRQYVYNVAKACDEGHCTAKDCAGVILYSAECATQVALDGIQCFGGNGY
INDFPMGRFLRDAKLYEIGAGTSEVRRLVIGRAFNAD
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 chain1ivh Chain A Residue 399 [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]
PDB1ivh Structure of human isovaleryl-CoA dehydrogenase at 2.6 A resolution: structural basis for substrate specificity,.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		R280 F283 F290 M293 Q348 C349 G352
Binding residue
(residue number reindexed from 1)		R275 F278 F285 M288 Q343 C344 G347
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) M135 S136 E254 A375 R387
Catalytic site (residue number reindexed from 1) M130 S131 E249 A370 R382
Enzyme Commision number 1.3.8.1: short-chain acyl-CoA dehydrogenase.
1.3.8.4: isovaleryl-CoA dehydrogenase.
Gene Ontology
Molecular Function
GO:0003995 acyl-CoA dehydrogenase activity
GO:0005515 protein binding
GO:0008470 3-methylbutanoyl-CoA dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors
GO:0016937 short-chain fatty acyl-CoA dehydrogenase activity
GO:0042802 identical protein binding
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0006552 L-leucine catabolic process
GO:0006631 fatty acid metabolic process
GO:0009083 branched-chain amino acid catabolic process
GO:0033539 fatty acid beta-oxidation using acyl-CoA dehydrogenase
Cellular Component
GO:0005654 nucleoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ivh, PDBe:1ivh, PDBj:1ivh
PDBsum1ivh
PubMed9214289
UniProtP26440|IVD_HUMAN Isovaleryl-CoA dehydrogenase, mitochondrial (Gene Name=IVD)

[Back to BioLiP]