4TOT | pdb_00004tot

Crystal structure of rat cyclophilin D in complex with a potent nonimmunosuppressive inhibitor

PDB DOI: https://doi.org/10.2210/pdb4TOT/pdb

Classification: ISOMERASE/ISOMERASE Inhibitor
Organism(s): Rattus norvegicus, synthetic construct
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-06-06 Released: 2014-11-12
Deposition Author(s): Knapp, M.S., Elling, R.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.230 (Depositor), 0.246 (DCC)
R-Value Work:
0.196 (Depositor), 0.211 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Potent nonimmunosuppressive cyclophilin inhibitors with improved pharmaceutical properties and decreased transporter inhibition.

Fu, J., Tjandra, M., Becker, C., Bednarczyk, D., Capparelli, M., Elling, R., Hanna, I., Fujimoto, R., Furegati, M., Karur, S., Kasprzyk, T., Knapp, M., Leung, K., Li, X., Lu, P., Mergo, W., Miault, C., Ng, S., Parker, D., Peng, Y., Roggo, S., Rivkin, A., Simmons, R.L., Wang, M., Wiedmann, B., Weiss, A.H., Xiao, L., Xie, L., Xu, W., Yifru, A., Yang, S., Zhou, B., Sweeney, Z.K.

(2014) J Med Chem 57: 8503-8516

PubMed: 25310383 Search on PubMed
DOI: https://doi.org/10.1021/jm500862r
Primary Citation Related Structures:
4TOT

PubMed Abstract:
Nonimmunosuppressive cyclophilin inhibitors have demonstrated efficacy for the treatment of hepatitis C infection (HCV). However, alisporivir, cyclosporin A, and most other cyclosporins are potent inhibitors of OATP1B1, MRP2, MDR1, and other important drug transporters. Reduction of the side chain hydrophobicity of the P4 residue preserves cyclophilin binding and antiviral potency while decreasing transporter inhibition. Representative inhibitor 33 (NIM258) is a less potent transporter inhibitor relative to previously described cyclosporins, retains anti-HCV activity in cell culture, and has an acceptable pharmacokinetic profile in rats and dogs. An X-ray structure of 33 bound to rat cyclophilin D is reported.

Organizational Affiliation

Novartis Institutes for Biomedical Research , 4560 Horton Street, Emeryville, California 94608, United States.

Macromolecule Content

Total Structure Weight: 77.54 kDa
Atom Count: 5,740
Modeled Residue Count: 700
Deposited Residue Count: 704
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase F, mitochondrial	A, B, C, D	165	Rattus norvegicus	Mutation(s): 1 Gene Names: Ppif EC: 5.2.1.8
UniProt
Find proteins for P29117 (Rattus norvegicus) Explore P29117 Go to UniProtKB: P29117
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29117
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
nonimmunosuppressive inhibitor	E, F, G, H	11	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain N [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth D]	I [auth A], K [auth B], M [auth C], N [auth D]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain N [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B]	J [auth A], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain J [auth A] Focus chain L [auth B] Interactions & Density Focus chain J [auth A] Focus chain L [auth B]

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
33X Query on 33X	E, F, G, H	D-PEPTIDE LINKING	C₄ H₉ N O₂		--
34E Query on 34E	E, F, G, H	L-PEPTIDE LINKING	C₁₃ H₂₇ N₃ O₃		VAL
ABA Query on ABA	E, F, G, H	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
BMT Query on BMT	E, F, G, H	L-PEPTIDE LINKING	C₁₀ H₁₉ N O₃		THR
DAL Query on DAL	E, F, G, H	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
MLE Query on MLE	E, F, G, H	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
MVA Query on MVA	E, F, G, H	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002115 Query on PRD_002115	E, F, G, H	nonimmunosuppressive inhibitor	Cyclic peptide / Inhibitor		Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.230 (Depositor), 0.246 (DCC)
R-Value Work: 0.196 (Depositor), 0.211 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.197	α = 89.95
b = 57.286	β = 83.81
c = 75.274	γ = 89.86

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-11-12

Deposition Author(s):

Knapp, M.S.

Elling, R.A.

Revision History (Full details and data files)

Version 1.0: 2014-11-12
Type: Initial release
Version 1.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.2: 2024-04-03
Changes: Refinement description