Structure of PDB 4qtf Chain A Binding Site BS01

Receptor Information
>4qtf Chain A (length=349) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPD
GLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMP
GDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREV
RWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATAD
DNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTY
GVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVS
PSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAK
Ligand information
Ligand IDMLD
InChIInChI=1S/C37H59N7O20/c1-13(30(51)44-20(35(58)59)9-10-23(48)43-19(8-6-7-18(38)34(56)57)32(53)40-14(2)33(54)55)39-31(52)15(3)61-29-25(42-17(5)47)36-60-12-22(63-36)28(29)64-37-24(41-16(4)46)27(50)26(49)21(11-45)62-37/h13-15,18-22,24-29,36-37,45,49-50H,6-12,38H2,1-5H3,(H,39,52)(H,40,53)(H,41,46)(H,42,47)(H,43,48)(H,44,51)(H,54,55)(H,56,57)(H,58,59)/t13-,14+,15+,18+,19-,20+,21+,22+,24+,25+,26+,27+,28+,29+,36+,37-/m0/s1
InChIKeyUPFMKPIBAIPLHT-RSJSDIDPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@H](C(=O)O)N)C(=O)N[C@H](C)C(=O)O)C(=O)O)NC(=O)[C@@H](C)O[C@@H]1[C@H]([C@@H]2OC[C@H]([C@H]1O[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)NC(=O)C)O2)NC(=O)C
OpenEye OEToolkits 1.5.0CC(C(=O)NC(CCC(=O)NC(CCCC(C(=O)O)N)C(=O)NC(C)C(=O)O)C(=O)O)NC(=O)C(C)OC1C(C2OCC(C1OC3C(C(C(C(O3)CO)O)O)NC(=O)C)O2)NC(=O)C
ACDLabs 10.04O=C(O)C(NC(=O)C(NC(=O)CCC(C(=O)O)NC(=O)C(NC(=O)C(OC3C(OC1OC(CO)C(O)C(O)C1NC(=O)C)C2OC(OC2)C3NC(=O)C)C)C)CCCC(C(=O)O)N)C
CACTVS 3.341C[CH](NC(=O)[CH](CCC[CH](N)C(O)=O)NC(=O)CC[CH](NC(=O)[CH](C)NC(=O)[CH](C)O[CH]1[CH](NC(C)=O)[CH]2OC[CH](O2)[CH]1O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3NC(C)=O)C(O)=O)C(O)=O
CACTVS 3.341C[C@@H](NC(=O)[C@H](CCC[C@@H](N)C(O)=O)NC(=O)CC[C@@H](NC(=O)[C@H](C)NC(=O)[C@@H](C)O[C@@H]1[C@@H](NC(C)=O)[C@@H]2OC[C@@H](O2)[C@H]1O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3NC(C)=O)C(O)=O)C(O)=O
FormulaC37 H59 N7 O20
NameGLCNAC(BETA1-4)-MURNAC(1,6-ANHYDRO)-L-ALA-GAMMA-D-GLU-MESO-A2PM-D-ALA;
2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE(BETA1-4)-2-ACETAMIDO-1,6-ANHYDRO-3-O-[(R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSE-L-ALANYL-GAMMA-D-GLUTAMYL-MESO-DIAMINOPIMELYL-D-ALANINE
ChEMBL
DrugBankDB04736
ZINCZINC000096006131
PDB chain4qtf Chain A Residue 501 [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]
PDB4qtf Structure and specificity of L-D-Transpeptidase from Mycobacterium tuberculosis and antibiotic resistance: Calcium binding promotes dimer formation
Resolution2.0 Å
Binding residue
(original residue number in PDB)		L62 T63 A64 S65 R139
Binding residue
(residue number reindexed from 1)		L4 T5 A6 S7 R81
Annotation score1
Enzymatic activity
Enzyme Commision number 2.3.2.-
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0016746 acyltransferase activity
GO:0046872 metal ion binding
GO:0071972 peptidoglycan L,D-transpeptidase activity
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0018104 peptidoglycan-protein cross-linking
GO:0071555 cell wall organization
Cellular Component
GO:0005886 plasma membrane

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4qtf, PDBe:4qtf, PDBj:4qtf
PDBsum4qtf
PubMed
UniProtI6Y9J2|LDT2_MYCTU L,D-transpeptidase 2 (Gene Name=ldtB)

[Back to BioLiP]