5K7K | pdb_00005k7k

Design and Optimization of Biaryl Ether Aryl Sulfonamides as Selective Inhibitors of NaV1.7: Discovery of Clinical Candidate PF-05089771


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.272 (Depositor), 0.295 (DCC) 
  • R-Value Work: 
    0.224 (Depositor) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Discovery of Clinical Candidate 4-[2-(5-Amino-1H-pyrazol-4-yl)-4-chlorophenoxy]-5-chloro-2-fluoro-N-1,3-thiazol-4-ylbenzenesulfonamide (PF-05089771): Design and Optimization of Diaryl Ether Aryl Sulfonamides as Selective Inhibitors of NaV1.7.

Swain, N.A.Batchelor, D.Beaudoin, S.Bechle, B.M.Bradley, P.A.Brown, A.D.Brown, B.Butcher, K.J.Butt, R.P.Chapman, M.L.Denton, S.Ellis, D.Galan, S.R.G.Gaulier, S.M.Greener, B.S.de Groot, M.J.Glossop, M.S.Gurrell, I.K.Hannam, J.Johnson, M.S.Lin, Z.Markworth, C.J.Marron, B.E.Millan, D.S.Nakagawa, S.Pike, A.Printzenhoff, D.Rawson, D.J.Ransley, S.J.Reister, S.M.Sasaki, K.Storer, R.I.Stupple, P.A.West, C.W.

(2017) J Med Chem 60: 7029-7042

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00598
  • Primary Citation Related Structures: 
    5K7K

  • PubMed Abstract: 

    A series of acidic diaryl ether heterocyclic sulfonamides that are potent and subtype selective Na V 1.7 inhibitors is described. Optimization of early lead matter focused on removal of structural alerts, improving metabolic stability and reducing cytochrome P450 inhibition driven drug-drug interaction concerns to deliver the desired balance of preclinical in vitro properties. Concerns over nonmetabolic routes of clearance, variable clearance in preclinical species, and subsequent low confidence human pharmacokinetic predictions led to the decision to conduct a human microdose study to determine clinical pharmacokinetics. The design strategies and results from preclinical PK and clinical human microdose PK data are described leading to the discovery of the first subtype selective Na V 1.7 inhibitor clinical candidate PF-05089771 (34) which binds to a site in the voltage sensing domain.


  • Organizational Affiliation
    • Icagen Inc. , 4222 Emperor Blvd no. 350, Durham, North Carolina 27703, United States.

Macromolecule Content 

  • Total Structure Weight: 55.4 kDa 
  • Atom Count: 3,756 
  • Modeled Residue Count: 455 
  • Deposited Residue Count: 477 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome P450 2C9477Homo sapiensMutation(s): 0 
Gene Names: CYP2C9CYP2C10
EC: 1.14.13.80 (PDB Primary Data), 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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11712
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
6RJ

Query on 6RJ



Download:Ideal Coordinates CCD File
C [auth A]4-[4-chloranyl-2-(1~{H}-pyrazol-4-yl)phenoxy]-3-cyano-~{N}-(1,3-thiazol-2-yl)benzenesulfonamide
C19 H12 Cl N5 O3 S2
XPZRWGQUAVWXIG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6RJ BindingDB:  5K7K IC50: 36 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.272 (Depositor), 0.295 (DCC) 
  • R-Value Work:  0.224 (Depositor) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.69α = 90
b = 91.69β = 90
c = 169.88γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description