4JP4 | pdb_00004jp4

Mmp13 in complex with a reverse hydroxamate Zn-binder

PDB DOI: https://doi.org/10.2210/pdb4JP4/pdb

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

Deposited: 2013-03-19 Released: 2014-03-05
Deposition Author(s): Gerhardt, S., Hargreaves, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free:
0.175 (Depositor), 0.193 (DCC)
R-Value Work:
0.151 (Depositor)
R-Value Observed:
0.152 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Hydantoin based inhibitors of MMP13--discovery of AZD6605.

De Savi, C., Waterson, D., Pape, A., Lamont, S., Hadley, E., Mills, M., Page, K.M., Bowyer, J., Maciewicz, R.A.

(2013) Bioorg Med Chem Lett 23: 4705-4712

PubMed: 23810497 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2013.05.089
Primary Citation Related Structures:
4JP4, 4JPA

PubMed Abstract:
Piperidine ether and aryl piperazine hydantoins are reported as potent inhibitors of MMP13. A medicinal chemistry campaign focused on replacing the reverse hydroxamate zinc binding group associated with historical inhibitors with a hydantoin zinc binding group then optimising MMP13 potency, solubility and DMPK properties whilst maintaining good selectivity over MMP14. A number of high quality candidates were progressed and following rat and dog safety evaluation, AZD6605 (3m) was identified as a candidate drug.

Organizational Affiliation

Oncology Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, USA. chris.desavi2@astrazeneca.com

Macromolecule Content

Total Structure Weight: 40.53 kDa
Atom Count: 3,234
Modeled Residue Count: 331
Deposited Residue Count: 346
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagenase 3	A, B	173	Homo sapiens	Mutation(s): 0 Gene Names: MMP13 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P45452
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AZ4 Query on AZ4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain N [auth B] MOL2 format, chain H [auth A] MOL2 format, chain N [auth B] mmCIF format, chain H [auth A] mmCIF format, chain N [auth B]	H [auth A], N [auth B]	N-[(2S)-4-(5-fluoropyrimidin-2-yl)-1-({4-[5-(2,2,2-trifluoroethoxy)pyrimidin-2-yl]piperazin-1-yl}sulfonyl)butan-2-yl]-N-hydroxyformamide C₁₉ H₂₃ F₄ N₇ O₅ S BEMGDWJRAZUSRP-HNNXBMFYSA-N		Interactions Focus chain H [auth A] Focus chain N [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], E [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain F [auth A] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain D [auth A]	D [auth A], F [auth A], K [auth B], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain K [auth B] Focus chain L [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain M [auth B]