3LJZ

Crystal Structure of Human MMP-13 complexed with an Amino-2-indanol compound

PDB DOI: https://doi.org/10.2210/pdb3LJZ/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-01-26 Released: 2011-02-02
Deposition Author(s): Shieh, H.-S., Kiefer, J.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.228
R-Value Work: 0.202
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure analysis reveals the flexibility of the ADAMTS-5 active site.

Shieh, H.S., Tomasselli, A.G., Mathis, K.J., Schnute, M.E., Woodard, S.S., Caspers, N., Williams, J.M., Kiefer, J.R., Munie, G., Wittwer, A., Malfait, A.M., Tortorella, M.D.

(2011) Protein Sci 20: 735-744

PubMed: 21370305 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/pro.606
Primary Citation of Related Structures:
3LJT, 3LJZ

PubMed Abstract:
A ((1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl) succinamide derivative (here referred to as Compound 12) shows significant activity toward many matrix metalloproteinases (MMPs), including MMP-2, MMP-8, MMP-9, and MMP-13. Modeling studies had predicted that this compound would not bind to ADAMTS-5 (a disintegrin and metalloproteinase with thrombospondin motifs-5) due to its shallow S1' pocket. However, inhibition analysis revealed it to be a nanomolar inhibitor of both ADAMTS-4 and -5. The observed inconsistency was explained by analysis of crystallographic structures, which showed that Compound 12 in complex with the catalytic domain of ADAMTS-5 (cataTS5) exhibits an unusual conformation in the S1' pocket of the protein. This first demonstration that cataTS5 can undergo an induced conformational change in its active site pocket by a molecule like Compound 12 should enable the design of new aggrecanase inhibitors with better potency and selectivity profiles.

Organizational Affiliation

Pfizer Global Research and Development, St. Louis, Missouri 63017, USA. shiehouse@sbcglobal.net

Macromolecule Content

Total Structure Weight: 78.23 kDa
Atom Count: 5,778
Modelled Residue Count: 653
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
Collagenase 3	A, B, C, D	164	Homo sapiens	Mutation(s): 1 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P45452
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LA3 Query on LA3 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain S [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain S [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain S [auth B]	AA [auth C], K [auth A], KA [auth D], S [auth B]	(2R)-2-[4-(1,3-benzodioxol-5-yl)benzyl]-N~4~-hydroxy-N~1~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide C₂₇ H₂₆ N₂ O₆ MJTVUROZTDIMFT-MZEQIWSPSA-N		Interactions Focus chain AA [auth C] Focus chain K [auth A] Focus chain KA [auth D] Focus chain S [auth B] Interactions & Density Focus chain AA [auth C] Focus chain K [auth A] Focus chain KA [auth D] Focus chain S [auth B]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain P [auth B] SDF format, chain X [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain X [auth C] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain X [auth C]	FA [auth D], GA [auth D], P [auth B], X [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain GA [auth D] Focus chain P [auth B] Focus chain X [auth C] Interactions & Density Focus chain FA [auth D] Focus chain GA [auth D] Focus chain P [auth B] 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 JA [auth D] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain Y [auth C] 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 JA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Y [auth C] 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 JA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth C]	HA [auth D] I [auth A] IA [auth D] J [auth A] JA [auth D] HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], Q [auth B], R [auth B], Y [auth C], 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 JA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C] 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 JA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain Y [auth C] Focus chain Z [auth C]
ZN Query on ZN 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 H [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain V [auth C] 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 H [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain V [auth C] 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 H [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C]	DA [auth D] EA [auth D] G [auth A] H [auth A] N [auth B] DA [auth D], EA [auth D], G [auth A], H [auth A], N [auth B], O [auth B], V [auth C], W [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain V [auth C] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain EA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain V [auth C] Focus chain W [auth C]
CA Query on CA 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 L [auth B] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain U [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 L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain U [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 L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	BA [auth D] CA [auth D] E [auth A] F [auth A] L [auth B] BA [auth D], CA [auth D], E [auth A], F [auth A], L [auth B], M [auth B], T [auth C], U [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-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 L [auth B] Focus chain M [auth B] Focus chain T [auth C] Focus chain U [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 L [auth B] Focus chain M [auth B] Focus chain T [auth C] Focus chain U [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
LA3	PDBBind: 3LJZ	Ki: 7.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.228
R-Value Work: 0.202
R-Value Observed: 0.203
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.604	α = 90
b = 94.927	β = 90
c = 120.406	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-02-02

Deposition Author(s):

Shieh, H.-S.

Kiefer, J.R.

Revision History (Full details and data files)

Version 1.0: 2011-02-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations