Structure of PDB 6lpy Chain B Binding Site BS02

Receptor Information
>6lpy Chain B (length=607) Species: 1772 (Mycolicibacterium smegmatis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHYKSNVRDQVFNLFEVFGVDKVLGADKFSDLDADTAREMLTEIARLAEG
PIAESFVEGDRNPPVFDPETHTVTLPEGFKKSMRALFDGGWDKVGLAEHL
GGIPMPRALQWALIEHILGANPAAYMYAMGPGMSEIFYNNGTDEQKKWAT
IAAERGWGATMVLTEPDAGSDVGAGRTKAVQQPDGTWHIEGVKRFITSAD
SDDLFENIMHLVLARPEGAGPGTKGLSLFFVPKFHFDHETGEIGERNGVF
VTNVEHKMGLKVSATCELSLGQHGIPAVGWLVGEVHNGIAQMFDVIEQAR
MMVGTKAIATLSTGYLNALEYAKERVQGADMTQMTDKTAPRVTITHHPDV
RRSLMTQKAYAEGLRAIYLYTATFQDAEVAQAVHGVDGDLAARVNDLLLP
IVKGFGSETAYAKLTESLQTLGGSGFLQDYPIEQYIRDSKIDSLYAGTTA
IQAQDFFFRKIIRDKGQALAYVAGEIEQFIKNNGRLKTERELLATALADV
QGMAASLTGYLMAAQEDAASIYKVGLGSVRFLMAVGDLLSGWLLARQAAV
AIEKLDAGATGADKSFYEGKIAAASFFAKNMLPLLTSTRQIIENLDNDVM
ELDEAAF
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 chain6lpy Chain B Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6lpy Structural basis for the broad substrate specificity of two acyl-CoA dehydrogenases FadE5 from mycobacteria.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		M162 L164 T165 G170 S171 F196 I197 T198 I442 Y446 T449
Binding residue
(residue number reindexed from 1)		M161 L163 T164 G169 S170 F195 I196 T197 I441 Y445 T448
Annotation score3
Enzymatic activity
Enzyme Commision number 1.3.8.1: short-chain acyl-CoA dehydrogenase.
1.3.8.7: medium-chain acyl-CoA dehydrogenase.
1.3.8.8: long-chain-acyl-CoA dehydrogenase.
Gene Ontology
Molecular Function
GO:0004466 long-chain fatty acyl-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:0070991 medium-chain fatty acyl-CoA dehydrogenase activity
Biological Process
GO:0006631 fatty acid metabolic process
Cellular Component
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6lpy, PDBe:6lpy, PDBj:6lpy
PDBsum6lpy
PubMed32601219
UniProtQ3L887|FADE5_MYCS2 Broad-specificity linear acyl-CoA dehydrogenase FadE5 (Gene Name=fadE5)

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