Structure of PDB 6sda Chain B Binding Site BS02

Receptor Information
>6sda Chain B (length=503) Species: 264462 (Bdellovibrio bacteriovorus HD100) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NFYQDGPQLSNTFRSDEALQKILKSLLPADAQKVALPHLEHLGERAVTDM
LTWAQEAESQPPVHVPFDPWGRRIDDIKTSHGWKALEKVAAEEGIVATAY
DRRFGAASRVYQMALLYLYSPSSAIFSCPLAMTDGAARALELYADADLKA
RVLPHLLSRDPKTFWTAGQWMTERTGGSDVSGTSTDAHPFTGTSEFGATH
SLHGTKWFTSATTSQMALTLARPDGAAPGSRGLSLFFLELRNDKGELNHI
QIHRLKDKLGTKALPTAELSLQGTPARMIGGVGEGVKRIASVLNITRIYN
SICAVGHIRRALDLAQDYSGKRQAFGKLLKDHPLHKSTLDSLEADFRKCI
AFSFFVANLLGQEEVGEASASEKILLRVLTPILKLYTAKKSIHISSEVVE
MFGGAGYVEDTGIPRLLRDAQVFSIWEGTTNVLSLDMLRAFEKDQAGQIL
EQFLVLNEAGSEELVRLQKLLTLSGEQKEQHAREIAFLIGNAVARIAMKK
YSL
Ligand information
Ligand IDMFK
InChIInChI=1S/C31H54N7O17P3S/c1-4-5-6-7-8-9-10-11-22(40)59-15-14-33-21(39)12-13-34-29(43)26(42)31(2,3)17-52-58(49,50)55-57(47,48)51-16-20-25(54-56(44,45)46)24(41)30(53-20)38-19-37-23-27(32)35-18-36-28(23)38/h18-20,24-26,30,41-42H,4-17H2,1-3H3,(H,33,39)(H,34,43)(H,47,48)(H,49,50)(H2,32,35,36)(H2,44,45,46)/t20-,24-,25-,26+,30-/m1/s1
InChIKeyCNKJPHSEFDPYDB-HSJNEKGZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
CACTVS 3.385CCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
CACTVS 3.385CCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23
ACDLabs 12.01O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)CCCCCCCCC
OpenEye OEToolkits 1.7.6CCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
FormulaC31 H54 N7 O17 P3 S
Namedecanoyl-CoA
ChEMBL
DrugBank
ZINCZINC000096014554
PDB chain6sda Chain B Residue 601 [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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PDB6sda Target highlights in CASP13: Experimental target structures through the eyes of their authors.
Resolution1.87 Å
Binding residue
(original residue number in PDB)		C130 G179 S180 S232 V288 A292 L295 N296 R299 R379 W428 E429
Binding residue
(residue number reindexed from 1)		C128 G177 S178 S230 V286 A290 L293 N294 R297 R377 W426 E427
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) M173 T174 T298 R441
Catalytic site (residue number reindexed from 1) M171 T172 T296 R439
Enzyme Commision number 1.3.99.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003995 acyl-CoA dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors

View graph for
Molecular Function
External links
PDB RCSB:6sda, PDBe:6sda, PDBj:6sda
PDBsum6sda
PubMed31442339
UniProtQ6MJ59

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