Structure of PDB 6nvc Chain D Binding Site BS02

Receptor Information
>6nvc Chain D (length=227) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HGGTILVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKPVQTGTARGDD
DLAEVGRLAGVTQLAGLARYPQPMAPAAAAEHAGMALPARDQIVRLIADL
DRPGRLTLVEGAGGLLVELAEPGVTLRDVAVDVAAAALVVVTADLGTLNH
TKLTLEALAAQQVSCAGLVIGSWPDPPGLVAASNRSALARIAMVRAALPA
GAASLDAGDFAAMSAAAFDRNWVAGLV
Ligand information
Ligand IDL67
InChIInChI=1S/C16H18O5/c17-14(18)8-10-4-6-11(7-5-10)16(21)13-3-1-2-12(13)9-15(19)20/h4-7,12-13H,1-3,8-9H2,(H,17,18)(H,19,20)
InChIKeyMDWWEFDMQKFGKX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)C[C@@H]1CCC[C@H]1C(=O)c2ccc(CC(O)=O)cc2
OpenEye OEToolkits 2.0.7c1cc(ccc1CC(=O)O)C(=O)C2CCCC2CC(=O)O
CACTVS 3.385OC(=O)C[CH]1CCC[CH]1C(=O)c2ccc(CC(O)=O)cc2
ACDLabs 12.01C2C(C(c1ccc(cc1)CC(=O)O)=O)C(CC2)CC(=O)O
FormulaC16 H18 O5
Name{(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetic acid
ChEMBL
DrugBank
ZINC
PDB chain6nvc Chain C Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6nvc Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 6
Resolution2.25 Å
Binding residue
(original residue number in PDB)		T11 K15 T41 P71 A73 P74 A110 G111 V115
Binding residue
(residue number reindexed from 1)		T13 K17 T43 P73 A75 P76 A112 G113 V117
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T11 G12 K15 T16 K37 T41 G54 E108
Catalytic site (residue number reindexed from 1) T13 G14 K17 T18 K39 T43 G56 E110
Enzyme Commision number 6.3.3.3: dethiobiotin synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0004141 dethiobiotin synthase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0046872 metal ion binding
Biological Process
GO:0009102 biotin biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6nvc, PDBe:6nvc, PDBj:6nvc
PDBsum6nvc
PubMed
UniProtP9WPQ5|BIOD_MYCTU Dethiobiotin synthetase BioD (Gene Name=bioD)

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