5LH4

Trypsin inhibitors for the treatment of pancreatitis - cpd 1

• PDB DOI: https://doi.org/10.2210/pdb5LH4/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2016-07-08 Released: 2018-01-17 
• Deposition Author(s): Schiering, N., D'Arcy, A., Skaanderup, P., Simic, O., Brandl, T., Woelcke, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.179 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 

Starting Model: other

Literature

Trypsin inhibitors for the treatment of pancreatitis.

Brandl, T., Simic, O., Skaanderup, P.R., Namoto, K., Berst, F., Ehrhardt, C., Schiering, N., Mueller, I., Woelcke, J.

(2016) Bioorg Med Chem Lett 26: 4340-4344

• PubMed: 27476144 
• DOI: https://doi.org/10.1016/j.bmcl.2016.07.029
• Primary Citation of Related Structures:  
  5LGO, 5LH4, 5LH8


• PubMed Abstract: 
  

  Proline-based trypsin inhibitors occupying the S1-S2-S1' region were identified by an HTS screening campaign. It was discovered that truncation of the P1' moiety and appropriate extension into the S4 region led to highly potent trypsin inhibitors with excellent selectivity against related serine proteases and a favorable hERG profile.

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Organizational Affiliation: 

Novartis Pharma AG, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.15 kDa 
• Atom Count: 2,047 
• Modelled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic trypsin	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6W4	F [auth A]	(2~{S},4~{S})-1-[4-(aminomethyl)phenyl]carbonyl-4-(4-cyclopropyl-1,2,3-triazol-1-yl)-~{N}-(2,2-diphenylethyl)pyrrolidine-2-carboxamide C32 H34 N6 O2 YBZBHUMSHGXQNF-FIBWVYCGSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
DMS	B [auth A], C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.179 
• R-Value Work: 0.152 
• R-Value Observed: 0.154 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.585	α = 90
b = 58.235	β = 90
c = 66.666	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Schiering, N., D'Arcy, A., Skaanderup, P., Simic, O., Brandl, T., Woelcke, J.

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary