5IRV

Human cytochrome P450 17A1 bound to inhibitor VT-464

PDB DOI: 10.2210/pdb5IRV/pdb

Classification: OXIDOREDUCTASE, LYASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-03-14 Released: 2017-03-15
Deposition Author(s): Scott, E.E., Petrunak, E.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.248
R-Value Work: 0.195
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural and Functional Evaluation of Clinically Relevant Inhibitors of Steroidogenic Cytochrome P450 17A1.

Petrunak, E.M., Rogers, S.A., Aube, J., Scott, E.E.

(2017) Drug Metab Dispos 45: 635-645

PubMed: 28373265 Search on PubMedSearch on PubMed Central
DOI: 10.1124/dmd.117.075317
Primary Citation of Related Structures:
5IRQ, 5IRV

PubMed Abstract:

Human steroidogenic cytochrome P450 17A1 (CYP17A1) is a bifunctional enzyme that performs both hydroxylation and lyase reactions, with the latter required to generate androgens that fuel prostate cancer proliferation. The steroid abiraterone, the active form of the only CYP17A1 inhibitor approved by the Food and Drug Administration, binds the catalytic heme iron, nonselectively impeding both reactions and ultimately causing undesirable corticosteroid imbalance. Some nonsteroidal inhibitors reportedly inhibit the lyase reaction more than the preceding hydroxylase reaction, which would be clinically advantageous, but the mechanism is not understood. Thus, the nonsteroidal inhibitors seviteronel and orteronel and the steroidal inhibitors abiraterone and galeterone were compared with respect to their binding modes and hydroxylase versus lyase inhibition. Binding studies and X-ray structures of CYP17A1 with nonsteroidal inhibitors reveal coordination to the heme iron like the steroidal inhibitors. ( S )-seviteronel binds similarly to both observed CYP17A1 conformations. However, ( S )-orteronel and ( R )-orteronel bind to distinct CYP17A1 conformations that differ in a region implicated in ligand entry/exit and the presence of a peripheral ligand. To reconcile these binding modes with enzyme function, side-by-side enzymatic analysis was undertaken and revealed that neither the nonsteroidal seviteronel nor the ( S )-orteronel inhibitors demonstrated significant lyase selectivity, but the less potent ( R )-orteronel was 8- to 11-fold selective for lyase inhibition. While active-site iron coordination is consistent with competitive inhibition, conformational selection for binding of some inhibitors and the differential presence of a peripheral ligand molecule suggest the possibility of CYP17A1 functional modulation by features outside the active site.

Organizational Affiliation:

Department of Medicinal Chemistry, University of Kansas, Lawrence, Kansas scottee@umich.edu.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Steroid 17-alpha-hydroxylase/17,20 lyase	A, B, C, D	494	Homo sapiens	Mutation(s): 0 Gene Names: CYP17A1, CYP17, S17AH EC: 1.14.14.19 (PDB Primary Data), 4.1.2.30 (PDB Primary Data), 1.14.14.32 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P05093 (Homo sapiens) Explore P05093 Go to UniProtKB: P05093
PHAROS: P05093 GTEx: ENSG00000148795
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05093
Protein Feature View 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 E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Ligand Interaction
6D8 Query on 6D8 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	VT-464 C₁₈ H₁₇ F₄ N₃ O₃ ZBRAJOQFSNYJMF-SFHVURJKSA-N		Ligand Interaction