Structure of PDB 6nwn Chain D Binding Site BS01

Receptor Information
>6nwn 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 IDL6M
InChIInChI=1S/C30H37N5O10/c31-23-10-11-35(30(44)34-23)26-14-21(36)22(45-26)15-32-24(37)9-8-20(29(42)43)33-25(38)13-18-2-1-3-19(18)28(41)17-6-4-16(5-7-17)12-27(39)40/h4-7,10-11,18-22,26,36H,1-3,8-9,12-15H2,(H,32,37)(H,33,38)(H,39,40)(H,42,43)(H2,31,34,44)/t18-,19+,20-,21-,22+,26+/m0/s1
InChIKeyJVRVDICAIPFWFZ-BONAQRLYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(ccc1CC(=O)O)C(=O)C2CCCC2CC(=O)NC(CCC(=O)NCC3C(CC(O3)N4C=CC(=NC4=O)N)O)C(=O)O
CACTVS 3.385NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CNC(=O)CC[C@H](NC(=O)C[C@@H]3CCC[C@H]3C(=O)c4ccc(CC(O)=O)cc4)C(O)=O)O2
ACDLabs 12.01C(CC(C(=O)O)NC(CC2C(C(c1ccc(CC(=O)O)cc1)=O)CCC2)=O)C(NCC4C(CC(N3C=CC(=NC3=O)N)O4)O)=O
OpenEye OEToolkits 2.0.7c1cc(ccc1CC(=O)O)C(=O)C2CCCC2CC(=O)N[C@@H](CCC(=O)NC[C@@H]3[C@H](C[C@@H](O3)N4C=CC(=NC4=O)N)O)C(=O)O
CACTVS 3.385NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CNC(=O)CC[CH](NC(=O)C[CH]3CCC[CH]3C(=O)c4ccc(CC(O)=O)cc4)C(O)=O)O2
FormulaC30 H37 N5 O10
Name5'-{[N-({(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetyl)-L-gamma-glutamyl]amino}-2',5'-dideoxycytidine
ChEMBL
DrugBank
ZINC
PDB chain6nwn Chain D Residue 402 [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]
PDB6nwn Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with glutamic acid linked compound 10
Resolution2.005 Å
Binding residue
(original residue number in PDB)		T11 G12 P71 M72 A73 P74 V115 G169 S170 L196 P197 G199 A200 A201
Binding residue
(residue number reindexed from 1)		T13 G14 P73 M74 A75 P76 V117 G171 S172 L198 P199 G201 A202 A203
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6nwn, PDBe:6nwn, PDBj:6nwn
PDBsum6nwn
PubMed
UniProtP9WPQ5|BIOD_MYCTU Dethiobiotin synthetase BioD (Gene Name=bioD)

[Back to BioLiP]