4QKZ | pdb_00004qkz

X-ray structure of the catalytic domain of MMP-8 with the inhibitor ML115

PDB DOI: https://doi.org/10.2210/pdb4QKZ/pdb

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

Deposited: 2014-06-10 Released: 2015-06-17
Deposition Author(s): Pochetti, G., Montanari, R., Capelli, D., Tortorella, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.194 (Depositor), 0.200 (DCC)
R-Value Work:
0.170 (Depositor), 0.180 (DCC)
R-Value Observed:
0.172 (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

Bone-Seeking Matrix Metalloproteinase Inhibitors for the Treatment of Skeletal Malignancy.

Laghezza, A., Piemontese, L., Brunetti, L., Caradonna, A., Agamennone, M., Di Pizio, A., Pochetti, G., Montanari, R., Capelli, D., Tauro, M., Loiodice, F., Tortorella, P.

(2020) Pharmaceuticals (Basel) 13

PubMed: 32492898 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.3390/ph13060113
Primary Citation of Related Structures:
4QKZ

PubMed Abstract:
Matrix metalloproteinases (MMPs) are a family of enzymes involved at different stages of cancer progression and metastasis. We previously identified a novel class of bisphosphonic inhibitors, selective for MMPs crucial for bone remodeling, such as MMP-2. Due to the increasing relevance of specific MMPs at various stages of tumor malignancy, we focused on improving potency towards certain isoforms. Here, we tackled MMP-9 because of its confirmed role in tumor invasion, metastasis, angiogenesis, and immuno-response, making it an ideal target for cancer therapy. Using a computational analysis, we designed and characterized potent MMP-2/MMP-9 inhibitors. This is a promising approach to develop and clinically translate inhibitors that could be used in combination with standard care therapy for the treatment of skeletal malignancies.

Organizational Affiliation

Department of Pharmacy and Pharmaceutical Sciences, University of Bari "A. Moro", via E. Orabona 4, 70125 Bari, Italy.

Macromolecule Content

Total Structure Weight: 18.93 kDa
Atom Count: 1,469
Modelled Residue Count: 163
Deposited Residue Count: 163
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil collagenase	A	163	Homo sapiens	Mutation(s): 0 Gene Names: MMP8, CLG1 EC: 3.4.24.34
UniProt & NIH Common Fund Data Resources
Find proteins for P22894 (Homo sapiens) Explore P22894 Go to UniProtKB: P22894
PHAROS: P22894 GTEx: ENSG00000118113
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22894
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QZK Query on QZK Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	{[(biphenyl-4-ylsulfonyl)amino]methanediyl}bis(phosphonic acid) C₁₃ H₁₅ N O₈ P₂ S SZOCMHFDKYEXMY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]