5A5I

Cytochrome 2C9 P450 inhibitor complex

PDB DOI: https://doi.org/10.2210/pdb5A5I/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-06-18 Released: 2016-08-24
Deposition Author(s): Skerratt, S.E., de Groot, M.J., Phillips, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.245
R-Value Work: 0.212
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of a Novel Binding Pocket for Cyp 2C9 Inhibitors: Crystallography, Pharmacophore Modelling and Inhibitor Sar.

Skerratt, S.E., de Groot, M.J., Phillips, C.

(2016) Medchemcomm 7: 813

DOI: https://doi.org/10.1039/C6MD00011H

Macromolecule Content

Total Structure Weight: 55.32 kDa
Atom Count: 3,702
Modelled Residue Count: 453
Deposited Residue Count: 477
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 2C9	A	477	Homo sapiens	Mutation(s): 0 EC: 1.14.14.1 (UniProt), 1.14.14.53 (UniProt), 1.14.14.52 (UniProt), 1.14.14.51 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11712 (Homo sapiens) Explore P11712 Go to UniProtKB: P11712
PHAROS: P11712 GTEx: ENSG00000138109
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11712
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A]
XI1 Query on XI1 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]	N-[4-(3-chloranyl-4-cyano-phenoxy)cyclohexyl]-1,1,1-tris(fluoranyl)methanesulfonamide C₁₄ H₁₄ Cl F₃ N₂ O₃ S AMFHXCAGSKYZAM-XYPYZODXSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.245
R-Value Work: 0.212
R-Value Observed: 0.214
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.217	α = 90
b = 92.217	β = 90
c = 170.414	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-08-24

Deposition Author(s):

Skerratt, S.E.

de Groot, M.J.

Phillips, C.

Revision History (Full details and data files)

Version 1.0: 2016-08-24
Type: Initial release
Version 1.1: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other

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Validate Data

Deposit Data

Help and Resources

5A5I

Cytochrome 2C9 P450 inhibitor complex

Discovery of a Novel Binding Pocket for Cyp 2C9 Inhibitors: Crystallography, Pharmacophore Modelling and Inhibitor Sar.

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)