2WO9

MMP12 complex with a beta hydroxy carboxylic acid

PDB DOI: https://doi.org/10.2210/pdb2WO9/pdb

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

Deposited: 2009-07-22 Released: 2009-09-08
Deposition Author(s): Holmes, I.P., Gaines, S., Watson, S.P., Lorthioir, O., Walker, A., Baddeley, S.J., Herbert, S., Egan, D., Convery, M.A., Singh, O.M.P., Gross, J.W., Strelow, J.M., Smith, R.H., Amour, A.J., Brown, D., Martin, S.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.218
R-Value Work: 0.172
R-Value Observed: 0.174

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

The Identification of Beta-Hydroxy Carboxylic Acids as Selective Mmp-12 Inhibitors.

Holmes, I.P., Gaines, S., Watson, S.P., Lorthioir, O., Walker, A., Baddeley, S.J., Herbert, S., Egan, D., Convery, M.A., Singh, O.M.P., Gross, J.W., Strelow, J.M., Smith, R.H., Amour, A.J., Brown, D., Martin, S.L.

(2009) Bioorg Med Chem Lett 19: 5760

PubMed: 19703773 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.07.155
Primary Citation of Related Structures:
2WO8, 2WO9, 2WOA

PubMed Abstract:
A new class of selective MMP-12 inhibitors have been identified via high throughput screening. Crystallization with MMP-12 confirmed the mode of binding and allowed initial optimization to be carried out using classical structure based design.

Organizational Affiliation

GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom.

Macromolecule Content

Total Structure Weight: 76.28 kDa
Atom Count: 5,940
Modelled Residue Count: 648
Deposited Residue Count: 656
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MACROPHAGE METALLOELASTASE	A, B, C, D	164	Homo sapiens	Mutation(s): 0 EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens) Explore P39900 Go to UniProtKB: P39900
PHAROS: P39900 GTEx: ENSG00000262406
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P39900
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
023 Query on 023 Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain L [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain L [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain L [auth B]	AA [auth D], L [auth B]	N^2^-[(2R)-2-{(1S)-1-[FORMYL(HYDROXY)AMINO]ETHYL}-5-PHENYLPENTANOYL]-N,3-DIMETHYL-L-VALINAMIDE C₂₁ H₃₃ N₃ O₄ GHVMTHKJUAOZJP-CGTJXYLNSA-N		Interactions Focus chain AA [auth D] Focus chain L [auth B] Interactions & Density Focus chain AA [auth D] Focus chain L [auth B]
068 Query on 068 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain X [auth C] MOL2 format, chain H [auth A] MOL2 format, chain X [auth C] mmCIF format, chain H [auth A] mmCIF format, chain X [auth C]	H [auth A], X [auth C]	(3S)-5-(4'-ACETYLBIPHENYL-4-YL)-3-HYDROXYPENTANOIC ACID C₁₉ H₂₀ O₄ QSVVRYPBRVSBDL-SFHVURJKSA-N		Interactions Focus chain H [auth A] Focus chain X [auth C] Interactions & Density Focus chain H [auth A] Focus chain X [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain HA [auth D] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth C]	HA [auth D] I [auth A] IA [auth D] J [auth A] K [auth A] HA [auth D], I [auth A], IA [auth D], J [auth A], K [auth A], R [auth B], S [auth B], T [auth B], Z [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C] Interactions & Density Focus chain HA [auth D] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain Y [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain Y [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain Y [auth C]	FA [auth D], GA [auth D], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain Y [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C]	BA [auth D] CA [auth D] E [auth A] F [auth A] M [auth B] BA [auth D], CA [auth D], E [auth A], F [auth A], M [auth B], N [auth B], U [auth C], V [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain E [auth A] Focus chain F [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth C] Focus chain V [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain W [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain W [auth C] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain W [auth C]	DA [auth D] EA [auth D] G [auth A] O [auth B] P [auth B] DA [auth D], EA [auth D], G [auth A], O [auth B], P [auth B], Q [auth B], W [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain W [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
068	BindingDB: 2WO9	IC50: 62 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.218
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.352	α = 66.15
b = 65.291	β = 83.84
c = 69.356	γ = 71.38

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-09-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-09-08
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: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other