Structure of PDB 5dtw Chain A Binding Site BS01

Receptor Information
>5dtw Chain A (length=244) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMIGITQAEAVLTIELQRPERRNALNSQLVEELTQAIRKAGDGSARAIVL
TGQGTAFCAGADLSGDAFAADYPDRLIELHKAMDASPMPVVGAINGPAIG
AGLQLAMQCDLRVVAPDAFFQFPTSKYGLALDNWSIRRLSSLVGHGRARA
MLLSAEKLTAEIALHTGMANRIGTLADAQAWAAEIARLAPLAIQHAKRVL
NDDGAIEEAWPAHKELFDKAWGSQDVIEAQVARMEKRPPKFQGA
Ligand information
Ligand ID5F9
InChIInChI=1S/C41H74N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-32(50)69-25-24-43-31(49)22-23-44-39(53)36(52)41(2,3)27-62-68(59,60)65-67(57,58)61-26-30-35(64-66(54,55)56)34(51)40(63-30)48-29-47-33-37(42)45-28-46-38(33)48/h28-30,34-36,40,51-52H,4-27H2,1-3H3,(H,43,49)(H,44,53)(H,57,58)(H,59,60)(H2,42,45,46)(H2,54,55,56)/t30-,34-,35-,36-,40-/m1/s1
InChIKeyJYLSVNBJLYCSSW-DLATUHJOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCCCCCCCCCCCCCC(=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 12.01OP(O)(OC1C(OC(C1O)n2c3c(nc2)c(N)ncn3)COP(OP(OCC(C)(C)C(C(NCCC(NCCSC(CCCCCCCCCCCCCCCCCCC)=O)=O)=O)O)(=O)O)(O)=O)=O
OpenEye OEToolkits 1.9.2CCCCCCCCCCCCCCCCCCCC(=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
OpenEye OEToolkits 1.9.2CCCCCCCCCCCCCCCCCCCC(=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 3.385CCCCCCCCCCCCCCCCCCCC(=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
FormulaC41 H74 N7 O17 P3 S
NameArachinoyl-CoA
ChEMBL
DrugBank
ZINC
PDB chain5dtw Chain A Residue 301 [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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PDB5dtw THPP target assignment reveals EchA6 as an essential fatty acid shuttle in mycobacteria.
Resolution2.439 Å
Binding residue
(original residue number in PDB)		E19 R20 R21 A23 A58 A60 D61 L62 H79 D83 G99 A100 Y126 W133
Binding residue
(residue number reindexed from 1)		E20 R21 R22 A24 A59 A61 D62 L63 H80 D84 G100 A101 Y127 W134
Annotation score1
Binding affinityMOAD: Kd=3.5uM
PDBbind-CN: -logKd/Ki=5.46,Kd=3.5uM
Enzymatic activity
Catalytic site (original residue number in PDB) A60 D65 P72 I76 A100 Q103 P122 T123 L128 L130 D131 P210 W220
Catalytic site (residue number reindexed from 1) A61 D66 P73 I77 A101 Q104 P123 T124 L129 L131 D132 P211 W221
Enzyme Commision number 4.2.1.17: enoyl-CoA hydratase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0004300 enoyl-CoA hydratase activity
GO:0016829 lyase activity
GO:0016836 hydro-lyase activity
Biological Process
GO:0006631 fatty acid metabolic process
GO:0006635 fatty acid beta-oxidation
Cellular Component
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5dtw, PDBe:5dtw, PDBj:5dtw
PDBsum5dtw
PubMed27571973
UniProtP9WNP1|ECHA6_MYCTU Probable enoyl-CoA hydratase EchA6 (Gene Name=echA6)

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