5LGO | pdb_00005lgo

Trypsin inhibitors for the treatment of pancreatitis - cpd 15

• PDB DOI: https://doi.org/10.2210/pdb5LGO/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2016-07-07 Released: 2016-08-10 
• Deposition Author(s): Schiering, N., D'Arcy, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 
  0.197 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.176 (Depositor) 

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 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].
Novartis Pharma AG, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland.
Novartis Pharma AG, Cardio Metabolic Development Franchise, Novartis Campus, CH-4002 Basel, Switzerland.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.95 kDa 
• Atom Count: 2,021 
• Modeled 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 Membrane Entity: Yes
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6VZ	D [auth A]	(2~{S},4~{S})-1-[4-(aminomethyl)-3-methoxy-phenyl]carbonyl-4-[4-(2-cyclopropylethoxy)-6,8-dihydro-5~{H}-pyrido[3,4-d]pyrimidin-7-yl]-~{N}-methyl-pyrrolidine-2-carboxamide C27 H36 N6 O4 PZBPHXPZLFDRAP-REWPJTCUSA-N
DMS	B [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free:  0.197 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.232	α = 90
b = 55.232	β = 90
c = 106.981	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-10 
Deposition Author(s): Schiering, N., D'Arcy, A.

Revision History  

• Version 1.0: 2016-08-10
  Type: Initial release
  
• Version 1.1: 2016-08-24
  Changes: Database references
• Version 2.0: 2019-10-16
  Changes: Atomic model, Data collection
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary