8H78 | pdb_00008h78

Crystal structure of human MMP-2 catalytic domain in complex with inhibitor

PDB DOI: https://doi.org/10.2210/pdb8H78/pdb

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

Deposited: 2022-10-19 Released: 2023-01-18
Deposition Author(s): Kamitani, M., Takeuchi, T., Mima, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.319 (Depositor), 0.322 (DCC)
R-Value Work:
0.265 (Depositor), 0.270 (DCC)
R-Value Observed:
0.268 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of TP0597850: A Selective, Chemically Stable, and Slow Tight-Binding Matrix Metalloproteinase-2 Inhibitor with a Phenylbenzamide-Pentapeptide Hybrid Scaffold.

Takeuchi, T., Nomura, Y., Tamita, T., Nishikawa, R., Kakinuma, H., Kojima, N., Hitaka, K., Tamura, Y., Kamitani, M., Mima, M., Nozoe, A., Hayashi, M.

(2023) J Med Chem 66: 822-836

PubMed: 36595440 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.2c01698
Primary Citation Related Structures:
8H78

PubMed Abstract:
Matrix metalloproteinase-2 (MMP2) is a zinc-dependent endopeptidase and a promising target for various diseases, including cancer and fibrosis. Herein, we report the discovery of a novel MMP2-selective inhibitor with high chemical stability and slow tight-binding features. Based on the degradation mechanism of our small-molecule-peptide hybrid 1 , the tripeptide linker {5-aminopentanoic acid [Ape(5)]-Glu-Asp} of 1 was replaced by a shorter linker (γ-D-Glu). Phenylbenzamide was suitable for the new generation of MMP2 inhibitors as an S1' pocket-binding group. The introduction of (4 S )-aminoproline dramatically increased the chemical stability while maintaining high subtype selectivity because of its interaction with Glu130. TP0597850 ( 18 ) exhibited high stability over a wide range of pH values as well as potent MMP2 inhibition ( K _i = 0.034 nM) and ≥2000-fold selectivity determined using the inhibition constants. A kinetic analysis revealed that it possesses slow tight-binding nature with a long MMP2 dissociative half-life ( t _1/2 = 265 min).

Organizational Affiliation

Taisho Pharmaceutical Co., Ltd., Saitama331-9530, Japan.

Macromolecule Content

Total Structure Weight: 40.05 kDa
Atom Count: 2,804
Modeled Residue Count: 335
Deposited Residue Count: 336
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix metalloproteinase-2	A, B	168	Homo sapiens	Mutation(s): 0 Gene Names: MMP2 EC: 3.4.24.24
UniProt & NIH Common Fund Data Resources
Find proteins for P08253 (Homo sapiens) Explore P08253 Go to UniProtKB: P08253
PHAROS: P08253 GTEx: ENSG00000087245
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08253
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L2U (Subject of Investigation/LOI) Query on L2U Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A]	I [auth A], O [auth B]	(2~{R})-2-[[4-[(4-aminocarbonylphenyl)carbonylamino]phenyl]sulfonylamino]-5-[(2~{S},4~{S})-4-azanyl-2-[[(2~{S})-1-[[(2~{S})-1-[(5-azanyl-5-oxidanylidene-pentyl)amino]-5-oxidanyl-1,5-bis(oxidanylidene)pentan-2-yl]-methyl-amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamoyl]pyrrolidin-1-yl]-5-oxidanylidene-pentanoic acid C₄₁ H₅₇ N₉ O₁₃ S XGGNDAOPHPLHFW-PVNIVXITSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Interactions & Density Focus chain I [auth A] Focus chain O [auth B]
2HP Query on 2HP Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	DIHYDROGENPHOSPHATE ION H₂ O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], J [auth B], K [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B] Focus chain K [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth A] L [auth B] M [auth B] E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]