1BMA

BENZYL METHYL AMINIMIDE INHIBITOR COMPLEXED TO PORCINE PANCREATIC ELASTASE

• PDB DOI: https://doi.org/10.2210/pdb1BMA/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 1995-05-01 Released: 1995-12-07 
• Deposition Author(s): Peisach, E., Casebier, D., Gallion, S.L., Furth, P., Petsko, G.A., Hogan Jr., J.C., Ringe, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.192 
• R-Value Observed: 0.192 

Literature

Interaction of a peptidomimetic aminimide inhibitor with elastase.

Peisach, E., Casebier, D., Gallion, S.L., Furth, P., Petsko, G.A., Hogan Jr., J.C., Ringe, D.

(1995) Science 269: 66-69

• PubMed: 7604279 
• DOI: https://doi.org/10.1126/science.7604279
• Primary Citation of Related Structures:  
  1BMA


• PubMed Abstract: 
  

  The crystal structure of an aminimide analog of a dipeptide inhibitor of porcine pancreatic elastase bound to its target serine protease has been solved. The peptidomimetic molecule binds in the same fashion as the class of dipeptides from which it was derived, making similar interactions with the subsites on the elastase surface. Because aminimides are readily synthesized from a wide variety of starting materials, they form the basis for a combinatorial chemistry approach to rational drug design.

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Organizational Affiliation: 

Program in Biophysics, Brandeis University, Waltham, MA 02254, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 26.59 kDa 
• Atom Count: 2,006 
• Modelled Residue Count: 240 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chymotrypsin-like elastase family member 1	A	240	Sus scrofa	Mutation(s): 0  EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa) Explore P00772  Go to UniProtKB:  P00772

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0QH	D [auth A]	(1R)-1-benzyl-1-methyl-1-(2-{[4-(1-methylethyl)phenyl]amino}-2-oxoethyl)-2-{(2S)-4-methyl-2-[(trifluoroacetyl)amino]pentanoyl}diazanium C27 H36 F3 N4 O3 HTEHUHSQPIQBEG-OHWKKVTOSA-O
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0QH	Binding MOAD:  1BMA	Ki: 2.60e+4 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000358 (0QH)	D [auth A]	(1R)-1-benzyl-1-methyl-1-(2-{[4-(1-methylethyl)phenyl]amino}-2-oxoethyl)-2-{(2S)-4-methyl-2-[(trifluoroacetyl) amino]pentanoyl}diazanium	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Work: 0.192 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.16	α = 90
b = 57.68	β = 90
c = 75.52	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-12-07 
Deposition Author(s): Peisach, E., Casebier, D., Gallion, S.L., Furth, P., Petsko, G.A., Hogan Jr., J.C., Ringe, D.

Revision History  

• Version 1.0: 1995-12-07
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other
• Version 1.4: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Structure summary