3IUB

Crystal structure of pantothenate synthetase from Mycobacterium tuberculosis in complex with 5-Methoxy-N-(5-methylpyridin-2-ylsulfonyl)-1H-indole-2-carboxamide

PDB DOI: https://doi.org/10.2210/pdb3IUB/pdb

Classification: LIGASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-08-31 Released: 2009-10-13
Deposition Author(s): Silvestre, H.L., Hung, A.W., Wen, S., Ciulli, A., Blundell, T.L., Abell, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.209
R-Value Work: 0.177
R-Value Observed: 0.179

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Application of fragment growing and fragment linking to the discovery of inhibitors of Mycobacterium tuberculosis pantothenate synthetase.

Hung, A.W., Silvestre, H.L., Wen, S., Ciulli, A., Blundell, T.L., Abell, C.

(2009) Angew Chem Int Ed Engl 48: 8452-8456

PubMed: 19780086 Search on PubMed
DOI: https://doi.org/10.1002/anie.200903821
Primary Citation of Related Structures:
3IMC, 3IME, 3IMG, 3ISJ, 3IUB, 3IUE, 3IVC, 3IVG, 3IVX

Organizational Affiliation

Department of Chemistry, University of Cambridge, UK.

Macromolecule Content

Total Structure Weight: 65.02 kDa
Atom Count: 5,094
Modelled Residue Count: 564
Deposited Residue Count: 602
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pantothenate synthetase	A, B	301	Mycobacterium tuberculosis	Mutation(s): 2 Gene Names: MT3707, MTCY07H7B.20, panC, Rv3602c EC: 6.3.2.1
UniProt
Find proteins for P9WIL5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIL5 Go to UniProtKB: P9WIL5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WIL5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FG2 Query on FG2 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B]	J [auth A], K [auth A], S [auth B]	5-methoxy-N-[(5-methylpyridin-2-yl)sulfonyl]-1H-indole-2-carboxamide C₁₆ H₁₅ N₃ O₄ S ZKUFSBNJBIOKLO-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain S [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
FG2	Binding MOAD: 3IUB	Kd: 2.90e+4 (nM) from 1 assay(s)
	BindingDB: 3IUB	Kd: 2.90e+4 (nM) from 1 assay(s)
	PDBBind: 3IUB	Kd: 2.90e+4 (nM) from 1 assay(s)