2WD2 | pdb_00002wd2

A chimeric microtubule disruptor with efficacy on a taxane resistant cell line

• PDB DOI: https://doi.org/10.2210/pdb2WD2/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-03-19 Released: 2010-03-31 
• Deposition Author(s): Leese, M.P., Jourdan, F.L., Kimberley, M.R., Cozier, G.E., Regis-Lydi, S., Foster, P.A., Newman, S.P., Thiyagarajan, N., Acharya, K.R., Ferrandis, E., Purohit, A., Reed, M.J., Potter, B.V.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 
  0.227 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Chimeric Microtubule Disruptors.

Leese, M.P., Jourdan, F.L., Kimberley, M.R., Cozier, G.E., Thiyagarajan, N., Stengel, C., Regis-Lydi, S., Foster, P.A., Newman, S.P., Acharya, K.R., Ferrandis, E., Purohit, A., Reed, M.J., Potter, B.V.L.

(2010) Chem Commun (Camb) 46: 2907

• PubMed: 20386818 
• DOI: https://doi.org/10.1039/c002558e
• Primary Citation Related Structures: 
  2WD2


• PubMed Abstract: 
  

  A chimeric approach is used to discover microtubule disruptors with excellent in vitro activity and oral bioavailability; a ligand-protein interaction with carbonic anhydrase that enhances bioavailability is characterised by protein X-ray crystallography. Dosing of a representative chimera in a tumour xenograft model confirms the excellent therapeutic potential of the class.

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Organizational Affiliation: 
• Medicinal Chemistry & Sterix Ltd., Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 29.81 kDa 
• Atom Count: 2,311 
• Modeled Residue Count: 254 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CARBONIC ANHYDRASE 2	A	259	Homo sapiens	Mutation(s): 0  EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MS5	C [auth A]	7-methoxy-2-(3-methoxybenzyl)-1,2,3,4-tetrahydroisoquinolin-6-yl sulfamate C18 H22 N2 O5 S BNHMNJHBVHWFAX-UHFFFAOYSA-N
ZN	B [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FMT	E [auth A], F [auth A], G [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free:  0.227 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.067	α = 90
b = 71.708	β = 90
c = 74.136	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-31 
Deposition Author(s): Leese, M.P., Jourdan, F.L., Kimberley, M.R., Cozier, G.E., Regis-Lydi, S., Foster, P.A., Newman, S.P., Thiyagarajan, N., Acharya, K.R., Ferrandis, E., Purohit, A., Reed, M.J., Potter, B.V.L.

Revision History  

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description