4A7B | pdb_00004a7b

MMP13 IN COMPLEX WITH A NOVEL SELECTIVE NON ZINC BINDING INHIBITOR CMPD22

• PDB DOI: https://doi.org/10.2210/pdb4A7B/pdb

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


• Deposited: 2011-11-11 Released: 2011-12-21 
• Deposition Author(s): Hargreaves, D., Gerhardt, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Lead Optimisation of Selective Non-Zinc Binding Inhibitors of Mmp13. Part 2.

De Savi, C., Morley, A.D., Nash, I., Karoutchi, G., Page, K., Ting, A., Gerhardt, S.

(2012) Bioorg Med Chem Lett 22: 271

• PubMed: 22153941 
• DOI: https://doi.org/10.1016/j.bmcl.2011.11.034
• Primary Citation Related Structures: 
  4A7B


• PubMed Abstract: 
  

  Directed screening has identified a novel series of non-zinc binding MMP13 inhibitors that possess good levels of activity whilst demonstrating excellent selectivity over related MMPs. A lead optimisation campaign has delivered compounds with enhanced MMP13 potency, good selectivity and acceptable bioavailability profiles leading to a predicted twice-a-day dosing regimen in man.

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Organizational Affiliation: 
• Respiratory and Inflammation Research Area, AstraZeneca, Mereside, Alderley Park, Macclesfield SK10 4TG, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 39.84 kDa 
• Atom Count: 2,963 
• Modeled Residue Count: 335 
• Deposited Residue Count: 338 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COLLAGENASE 3	A, B	169	Homo sapiens	Mutation(s): 0  EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for P45452 (Homo sapiens) Explore P45452  Go to UniProtKB:  P45452
PHAROS:  P45452 GTEx:  ENSG00000137745

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3W5	C [auth A]	N-[(3S)-1,1-dioxidotetrahydro-2H-thiopyran-3-yl]-4-(4-{[(3S)-3-hydroxy-1-azabicyclo[2.2.2]oct-3-yl]ethynyl}phenoxy)benzamide C27 H30 N2 O5 S IOEYWFCDGXVEFG-HOFKKMOUSA-N
3W4	K [auth B]	N-[(3R)-1,1-dioxidotetrahydro-2H-thiopyran-3-yl]-4-(4-{[(3S)-3-hydroxy-1-azabicyclo[2.2.2]oct-3-yl]ethynyl}phenoxy)benzamide C27 H30 N2 O5 S IOEYWFCDGXVEFG-KCWPFWIISA-N
GOL	E [auth A], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
HAE	D [auth A], L [auth B]	ACETOHYDROXAMIC ACID C2 H5 N O2 RRUDCFGSUDOHDG-UHFFFAOYSA-N
ZN	F [auth A], H [auth A], N [auth B], O [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	G [auth A], I [auth A], P [auth B], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	J [auth A], R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.253 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.854	α = 90
b = 36.22	β = 131.1
c = 95.568	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-21 
Deposition Author(s): Hargreaves, D., Gerhardt, S.

Revision History  

• Version 1.0: 2011-12-21
  Type: Initial release
  
• Version 1.1: 2012-01-11
  Changes: Other
• Version 1.2: 2018-04-04
  Changes: Data collection
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description