Structure of PDB 3fpa Chain B Binding Site BS01

Receptor Information
>3fpa Chain B (length=226) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HMTILVVTGTGTGVGKTVVCAALASAARQAGIDVAVCKPVQTGTARGDDD
LAEVGRLAGVTQLAGLARYPQPMAPAAAAEHAGMALPARDQIVRLIADLD
RPGRLTLVEGAGGLLVELAEPGVTLRDVAVDVAAAALVVVTADLGTLNHT
KLTLEALAAQQVSCAGLVIGSWPDPPGLVAASNRSALARIAMVRAALPAG
AASLDAGDFAAMSAAAFDRNWVAGLV
Ligand information
Ligand IDDTB
InChIInChI=1S/C10H18N2O3/c1-7-8(12-10(15)11-7)5-3-2-4-6-9(13)14/h7-8H,2-6H2,1H3,(H,13,14)(H2,11,12,15)/t7-,8+/m0/s1
InChIKeyAUTOLBMXDDTRRT-JGVFFNPUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1C(NC(=O)N1)CCCCCC(=O)O
OpenEye OEToolkits 1.7.6C[C@H]1[C@H](NC(=O)N1)CCCCCC(=O)O
CACTVS 3.385C[C@@H]1NC(=O)N[C@@H]1CCCCCC(O)=O
ACDLabs 12.01C1(=O)NC(C(N1)C)CCCCCC(=O)O
CACTVS 3.385C[CH]1NC(=O)N[CH]1CCCCCC(O)=O
FormulaC10 H18 N2 O3
Name6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID;
D-DESTHIOBIOTIN
ChEMBLCHEMBL1232381
DrugBankDB03775
ZINCZINC000094437777
PDB chain3fpa Chain A Residue 803 [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]
PDB3fpa Structural characterization of the Mycobacterium tuberculosis biotin biosynthesis enzymes 7,8-diaminopelargonic acid synthase and dethiobiotin synthetase.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		T11 T41 A73 A110 G111
Binding residue
(residue number reindexed from 1)		T12 T42 A74 A111 G112
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) T11 G12 K15 T16 K37 T41 G54 E108
Catalytic site (residue number reindexed from 1) T12 G13 K16 T17 K38 T42 G55 E109
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3fpa, PDBe:3fpa, PDBj:3fpa
PDBsum3fpa
PubMed20565114
UniProtP9WPQ5|BIOD_MYCTU Dethiobiotin synthetase BioD (Gene Name=bioD)

[Back to BioLiP]