4KTK

Crystal structure of Mycobacterium tuberculosis CYP121 in complex with 4-(3-amino-4-(4-hydroxyphenyl)-1H-pyrazol-5-yl)benzene-1,3-diol

PDB DOI: https://doi.org/10.2210/pdb4KTK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-05-20 Released: 2013-07-03
Deposition Author(s): Hudson, S.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.183
R-Value Work: 0.155
R-Value Observed: 0.157

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Overcoming the Limitations of Fragment Merging: Rescuing a Strained Merged Fragment Series Targeting Mycobacterium tuberculosis CYP121.

Hudson, S.A., Surade, S., Coyne, A.G., McLean, K.J., Leys, D., Munro, A.W., Abell, C.

(2013) ChemMedChem 8: 1451-1456

PubMed: 23788280 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/cmdc.201300219
Primary Citation of Related Structures:
4KTF, 4KTJ, 4KTK, 4KTL

Organizational Affiliation

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.

Macromolecule Content

Total Structure Weight: 44.55 kDa
Atom Count: 3,624
Modelled Residue Count: 395
Deposited Residue Count: 395
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 121	A	395	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: Rv2276, RVBD_2276 EC: 1.14
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
KTK Query on KTK Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	4-[3-amino-4-(4-hydroxyphenyl)-1H-pyrazol-5-yl]benzene-1,3-diol C₁₅ H₁₃ N₃ O₃ QJXCNANYVSBOBZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
SO4 Query on SO4 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] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.183
R-Value Work: 0.155
R-Value Observed: 0.157
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.77	α = 90
b = 77.77	β = 90
c = 263.6	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-07-03

Deposition Author(s):

Hudson, S.A.

Revision History (Full details and data files)

Version 1.0: 2013-07-03
Type: Initial release
Version 1.1: 2013-10-09
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

4KTK

Crystal structure of Mycobacterium tuberculosis CYP121 in complex with 4-(3-amino-4-(4-hydroxyphenyl)-1H-pyrazol-5-yl)benzene-1,3-diol

Overcoming the Limitations of Fragment Merging: Rescuing a Strained Merged Fragment Series Targeting Mycobacterium tuberculosis CYP121.

Entity ID: 1

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)