1MMJ

Porcine pancreatic elastase complexed with a potent peptidyl inhibitor, FR136706

PDB DOI: https://doi.org/10.2210/pdb1MMJ/pdb

Classification: HYDROLASE
Organism(s): Sus scrofa
Mutation(s): No

Deposited: 2002-09-04 Released: 2002-12-23
Deposition Author(s): Kinoshita, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.241
R-Value Work: 0.215
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

True interaction mode of porcine pancreatic elastase with FR136706, a potent peptidyl inhibitor

Kinoshita, T., Nakanishi, I., Sato, A., Tada, T.

(2003) Bioorg Med Chem Lett 13: 21-24

PubMed: 12467609 Search on PubMed
DOI: https://doi.org/10.1016/s0960-894x(02)00852-1
Primary Citation of Related Structures:
1MMJ

PubMed Abstract:
The crystal structure of porcine pancreatic elastase (PPE) complexed with a potent peptidyl inhibitor, FR136706, was solved at 2.2A resolution. FR136706 fits snugly into the extended active site pocket. The benzene moiety of FR136706 induced dramatic movement of the side chain moiety of Arg217 and both moieties formed a pi-pi interaction, which has never been found previously in structures of PPE complexed with inhibitors. This novel interaction mode may lead to design of new types of inhibitors.

Organizational Affiliation

Exploratory Research Laboratories, Fujisawa Pharmaceutical Co. Ltd., 5-2-3, Tokodai, Tsukuba, Ibaraki 300-2698, Japan. takayoshi_kinoshita@po.fujisawa.co.jp

Macromolecule Content

Total Structure Weight: 26.64 kDa
Atom Count: 2,137
Modelled Residue Count: 240
Deposited Residue Count: 240
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
elastase 1	A [auth N]	240	Sus scrofa	Mutation(s): 0 EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa) Explore P00772 Go to UniProtKB: P00772
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00772
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FR1 Query on FR1 Download Ideal Coordinates CCD File SDF format, chain D [auth N] MOL2 format, chain D [auth N] mmCIF format, chain D [auth N]	D [auth N]	2-[4-[[(S)-1-[[(S)-2-[[(RS)-3,3,3-TRIFLUORO-1-ISOPROPYL-2-OXOPROPYL]AMINOCARBONYL]PYRROLIDIN-1-YL-]CARBONYL]-2-METHYLPROPYL]AMINOCARBONYL]BENZOYLAMINO]ACETIC ACID C₂₆ H₃₃ F₃ N₄ O₇ MRTSIBBMOWLRPY-IHPCNDPISA-N		Interactions Focus chain D [auth N] Interactions & Density Focus chain D [auth N]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth N] MOL2 format, chain B [auth N] mmCIF format, chain B [auth N]	B [auth N]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth N] Interactions & Density Focus chain B [auth N]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth N] MOL2 format, chain C [auth N] mmCIF format, chain C [auth N]	C [auth N]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth N] Interactions & Density Focus chain C [auth N]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.241
R-Value Work: 0.215
R-Value Observed: 0.215
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.29	α = 90
b = 58.31	β = 90
c = 75.52	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2002-12-23

Deposition Author(s):

Kinoshita, T.

Revision History (Full details and data files)

Version 1.0: 2002-12-23
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary