3IVC

Crystal structure of pantothenate synthetase in complex with 2-(2-((benzofuran-2-ylmethoxy)carbonyl)-5-methoxy-1H-indol-1-yl)acetic acid

PDB DOI: https://doi.org/10.2210/pdb3IVC/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: 2.13 Å
R-Value Work: 0.165

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: 65.01 kDa
Atom Count: 4,811
Modelled Residue Count: 575
Deposited Residue Count: 602
Unique protein chains: 1

Macromolecules

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(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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FG4 Query on FG4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B]	C [auth A], K [auth B]	{2-[(1-benzofuran-2-ylmethoxy)carbonyl]-5-methoxy-1H-indol-1-yl}acetic acid C₂₁ H₁₇ N O₆ CKGFVKXFHXZPEW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A]	I [auth A], J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], O [auth B], P [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth B] Focus chain P [auth B]
EOH Query on EOH Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain Q [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth B]	N [auth B], Q [auth B]	ETHANOL C₂ H₆ O LFQSCWFLJHTTHZ-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Focus chain Q [auth B] Interactions & Density Focus chain N [auth B] Focus chain Q [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
FG4	PDBBind: 3IVC	Kd: 7.50e+4 (nM) from 1 assay(s)
FG4	Binding MOAD: 3IVC	Kd: 7.50e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Work: 0.165
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.19	α = 90
b = 69.96	β = 100.25
c = 82.17	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASES	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-10-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-10-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2021-10-13
Changes: Database references, Derived calculations
Version 1.3: 2023-09-06
Changes: Data collection, Refinement description

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Help and Resources

3IVC

Crystal structure of pantothenate synthetase in complex with 2-(2-((benzofuran-2-ylmethoxy)carbonyl)-5-methoxy-1H-indol-1-yl)acetic acid

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)