6IW7

structural insights into Mycobacterium tuberculosis ClpP1P2 inhibition by Cediranib: implications for developing antimicrobial agents targeting Clp protease

PDB DOI: https://doi.org/10.2210/pdb6IW7/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Mycobacterium tuberculosis CDC1551
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-12-04 Released: 2020-01-01
Deposition Author(s): Bao, R., Luo, Y.F., Zhu, Y.B., Yang, Y., Zhou, Y.Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.249
R-Value Work: 0.192
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Literature

structural insights into Mycobacterium tuberculosis ClpP1P2 inhibition by Cediranib: implications for developing antimicrobial agents targeting Clp protease

Bao, R., Luo, Y.F., Zhu, Y.B., Yang, Y., Yang, T.

To be published.

Macromolecule Content

Total Structure Weight: 311.39 kDa
Atom Count: 20,515
Modelled Residue Count: 2,593
Deposited Residue Count: 2,772
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 2	A C E [auth F] F [auth H] H [auth J] A, C, E [auth F], F [auth H], H [auth J], J [auth L], M [auth E]	202	Mycobacterium tuberculosis CDC1551	Mutation(s): 0 Gene Names: clpP2, MT2535 EC: 3.4.21.92
UniProt
Find proteins for P9WPC3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC3 Go to UniProtKB: P9WPC3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPC3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent Clp protease proteolytic subunit 1	B D G [auth I] I [auth K] K [auth M] B, D, G [auth I], I [auth K], K [auth M], L [auth N], N [auth G]	194	Mycobacterium tuberculosis CDC1551	Mutation(s): 0 Gene Names: clpP1, clpP, MT2536 EC: 3.4.21.92
UniProt
Find proteins for P9WPC5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC5 Go to UniProtKB: P9WPC5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPC5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AV3 (Subject of Investigation/LOI) Query on AV3 Download Ideal Coordinates CCD File SDF format, chain DA [auth I] SDF format, chain IA [auth K] SDF format, chain PA [auth N] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain UA [auth G] SDF format, chain W [auth D] MOL2 format, chain DA [auth I] MOL2 format, chain IA [auth K] MOL2 format, chain PA [auth N] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain UA [auth G] MOL2 format, chain W [auth D]	DA [auth I] IA [auth K] PA [auth N] Q [auth B] R [auth B] DA [auth I], IA [auth K], PA [auth N], Q [auth B], R [auth B], UA [auth G], W [auth D]	4-[(4-fluoro-2-methyl-3H-indol-5-yl)oxy]-6-methoxy-7-[3-(pyrrolidin-1-yl)propoxy]quinazoline C₂₅ H₂₇ F N₄ O₃ ZOVVOYNGCNKFNN-UHFFFAOYSA-N		Interactions Focus chain DA [auth I] Focus chain IA [auth K] Focus chain PA [auth N] Focus chain Q [auth B] Focus chain R [auth B] Focus chain UA [auth G] Focus chain W [auth D] Interactions & Density Focus chain DA [auth I] Focus chain IA [auth K] Focus chain PA [auth N] Focus chain Q [auth B] Focus chain R [auth B] Focus chain UA [auth G] Focus chain W [auth D]
S0R Query on S0R Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain EA [auth I] SDF format, chain GA [auth J] SDF format, chain JA [auth K] SDF format, chain LA [auth L] SDF format, chain NA [auth M] SDF format, chain O [auth A] SDF format, chain QA [auth N] SDF format, chain S [auth B] SDF format, chain SA [auth E] SDF format, chain U [auth C] SDF format, chain VA [auth G] SDF format, chain X [auth D] SDF format, chain Z [auth F] MOL2 format, chain BA [auth H] MOL2 format, chain EA [auth I] MOL2 format, chain GA [auth J] MOL2 format, chain JA [auth K] MOL2 format, chain LA [auth L] MOL2 format, chain NA [auth M] MOL2 format, chain O [auth A] MOL2 format, chain QA [auth N] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth E] MOL2 format, chain U [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth F]	BA [auth H] EA [auth I] GA [auth J] JA [auth K] LA [auth L] BA [auth H], EA [auth I], GA [auth J], JA [auth K], LA [auth L], NA [auth M], O [auth A], QA [auth N], S [auth B], SA [auth E], U [auth C], VA [auth G], X [auth D], Z [auth F]	(2S)-2-benzamido-4-methyl-pentanoic acid C₁₃ H₁₇ N O₃ POLGZPYHEPOBFG-NSHDSACASA-N		Interactions Focus chain BA [auth H] Focus chain EA [auth I] Focus chain GA [auth J] Focus chain JA [auth K] Focus chain LA [auth L] Focus chain NA [auth M] Focus chain O [auth A] Focus chain QA [auth N] Focus chain S [auth B] Focus chain SA [auth E] Focus chain U [auth C] Focus chain VA [auth G] Focus chain X [auth D] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth H] Focus chain EA [auth I] Focus chain GA [auth J] Focus chain JA [auth K] Focus chain LA [auth L] Focus chain NA [auth M] Focus chain O [auth A] Focus chain QA [auth N] Focus chain S [auth B] Focus chain SA [auth E] Focus chain U [auth C] Focus chain VA [auth G] Focus chain X [auth D] Focus chain Z [auth F]
LEU Query on LEU Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain CA [auth H] SDF format, chain FA [auth I] SDF format, chain HA [auth J] SDF format, chain KA [auth K] SDF format, chain MA [auth L] SDF format, chain OA [auth M] SDF format, chain P [auth A] SDF format, chain RA [auth N] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain V [auth C] SDF format, chain WA [auth G] SDF format, chain Y [auth D] MOL2 format, chain AA [auth F] MOL2 format, chain CA [auth H] MOL2 format, chain FA [auth I] MOL2 format, chain HA [auth J] MOL2 format, chain KA [auth K] MOL2 format, chain MA [auth L] MOL2 format, chain OA [auth M] MOL2 format, chain P [auth A] MOL2 format, chain RA [auth N] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain V [auth C] MOL2 format, chain WA [auth G] MOL2 format, chain Y [auth D]	AA [auth F] CA [auth H] FA [auth I] HA [auth J] KA [auth K] AA [auth F], CA [auth H], FA [auth I], HA [auth J], KA [auth K], MA [auth L], OA [auth M], P [auth A], RA [auth N], T [auth B], TA [auth E], V [auth C], WA [auth G], Y [auth D]	LEUCINE C₆ H₁₃ N O₂ ROHFNLRQFUQHCH-YFKPBYRVSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth H] Focus chain FA [auth I] Focus chain HA [auth J] Focus chain KA [auth K] Focus chain MA [auth L] Focus chain OA [auth M] Focus chain P [auth A] Focus chain RA [auth N] Focus chain T [auth B] Focus chain TA [auth E] Focus chain V [auth C] Focus chain WA [auth G] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth H] Focus chain FA [auth I] Focus chain HA [auth J] Focus chain KA [auth K] Focus chain MA [auth L] Focus chain OA [auth M] Focus chain P [auth A] Focus chain RA [auth N] Focus chain T [auth B] Focus chain TA [auth E] Focus chain V [auth C] Focus chain WA [auth G] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.69 Å
R-Value Free: 0.249
R-Value Work: 0.192
R-Value Observed: 0.193
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.634	α = 90
b = 180.78	β = 95.716
c = 95.926	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-01-01

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81473253

Revision History (Full details and data files)

Version 1.0: 2020-01-01
Type: Initial release
Version 2.0: 2020-04-29
Type: Coordinate replacement
Reason: Ligand geometry
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
Version 3.0: 2023-04-19
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Source and taxonomy, Structure summary
Version 3.1: 2023-11-29
Changes: Data collection, Refinement description

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6IW7

structural insights into Mycobacterium tuberculosis ClpP1P2 inhibition by Cediranib: implications for developing antimicrobial agents targeting Clp protease

structural insights into Mycobacterium tuberculosis ClpP1P2 inhibition by Cediranib: implications for developing antimicrobial agents targeting Clp protease

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

UniProt

Entity Groups

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)