4G46

Structure of cytochrome P450 CYP121 in complex with 4-oxo-4,5,6,7-tetrahydrobenzofuran-3-carboxylate

PDB DOI: https://doi.org/10.2210/pdb4G46/pdb

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

Deposited: 2012-07-16 Released: 2012-09-05
Deposition Author(s): Hudson, S.A., McLean, K.J., Surade, S., Yang, Y.-Q., Leys, D., Ciulli, A., Munro, A.W., Abell, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.172
R-Value Work: 0.149
R-Value Observed: 0.150

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Application of Fragment Screening and Merging to the Discovery of Inhibitors of the Mycobacterium tuberculosis Cytochrome P450 CYP121

Hudson, S.A., McLean, K.J., Surade, S., Yang, Y.-Q., Leys, D., Ciulli, A., Munro, A.W., Abell, C.

(2012) Angew Chem Int Ed Engl 51: 9311-9316

PubMed: 22890978 Search on PubMed
DOI: https://doi.org/10.1002/anie.201202544
Primary Citation of Related Structures:
4G1X, 4G2G, 4G44, 4G45, 4G46, 4G47, 4G48

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 44.49 kDa
Atom Count: 3,886
Modelled Residue Count: 395
Deposited Residue Count: 396
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 121	A	396	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: Rv2276 EC: 1.14 (PDB Primary Data), 1.14.19.70 (UniProt)
UniProt
Find proteins for P9WPP7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPP7 Go to UniProtKB: P9WPP7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WPP7
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]
TTY Query on TTY Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	4-oxo-4,5,6,7-tetrahydro-1-benzofuran-3-carboxylic acid C₉ H₈ O₄ FABBWECRHZNMDQ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.52 Å
R-Value Free: 0.172
R-Value Work: 0.149
R-Value Observed: 0.150
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.57	α = 90
b = 77.57	β = 90
c = 262.99	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-09-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-05
Type: Initial release
Version 1.1: 2012-09-19
Changes: Database references
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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Help and Resources

4G46

Structure of cytochrome P450 CYP121 in complex with 4-oxo-4,5,6,7-tetrahydrobenzofuran-3-carboxylate

Application of Fragment Screening and Merging to the Discovery of Inhibitors of the Mycobacterium tuberculosis Cytochrome P450 CYP121

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)