Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 78234.15 
• Atom Count: 5433 
• Residue Count: 656 
• Unique protein chains: 1

3LJZ

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

• DOI: 10.2210/pdb3LJZ/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 1 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.228 
• R-Value Work: 0.202 

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 
• DOI: 10.1002/pro.606
• Primary Citation of Related Structures:  
  3LJT


• 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.

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Organizational Affiliation: 

Pfizer Global Research and Development, St. Louis, Missouri 63017, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Collagenase 3	A, B, C, D	164	Homo sapiens	Mutation(s): 1  Gene Names: MMP13 EC: 3.4.24.-
Find proteins for P45452 (Homo sapiens) Go to Gene View: MMP13 Go to UniProtKB:  P45452

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EPE	B, C, D	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HEPES C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
ZN	A, B, C, D	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A, B, C, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
LA3	A, B, C, D	(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 (R)-2-(4-(benzo[d][1,3]dioxol-5-yl)benzyl)-N4-hydroxy-N1-((1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl) succinamide C27 H26 N2 O6 MJTVUROZTDIMFT-MZEQIWSPSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LA3	Ki: 7.3 nM BINDINGMOAD
LA3	Ki: 7.3 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.228 
• R-Value Work: 0.202 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 73.604	α = 90.00
b = 94.927	β = 90.00
c = 120.406	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History 

• Version 1.0: 2011-02-02
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2017-11-01
  Type: Refinement description