5LH8

Trypsin inhibitors for the treatment of pancreatitis - cpd 8

PDB DOI: https://doi.org/10.2210/pdb5LH8/pdb

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

Deposited: 2016-07-08 Released: 2016-08-10
Deposition Author(s): Schiering, N., D'Arcy, A., Skaanderup, P., Simic, O., Brandl, T., Woelcke, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.182
R-Value Work: 0.152
R-Value Observed: 0.154

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

Novartis Pharma AG, Novartis Institutes for BioMedical Research, Novartis Campus, CH-4002 Basel, Switzerland. Electronic address: trixi.brandl@novartis.com.

Macromolecule Content

Total Structure Weight: 24.06 kDa
Atom Count: 2,084
Modelled Residue Count: 223
Deposited Residue Count: 223
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00760
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6WH Query on 6WH Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	(2~{S},4~{S})-1-[4-(aminomethyl)-3-methoxy-phenyl]carbonyl-4-(4-cyclopropyl-1,2,3-triazol-1-yl)-~{N}-[(1~{S},2~{R})-2-phenylcyclohexyl]pyrrolidine-2-carboxamide C₃₁ H₃₈ N₆ O₃ AYVQDWAWTUYBGU-RVUATISTSA-N		Interactions Focus chain E [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.54 Å
R-Value Free: 0.182
R-Value Work: 0.152
R-Value Observed: 0.154
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.951	α = 90
b = 58.024	β = 90
c = 65.811	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-08-10
Type: Initial release
Version 1.1: 2016-08-24
Changes: Database references
Version 1.2: 2019-10-16
Changes: Data collection
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Structure summary