5MTK | pdb_00005mtk

Crystal structure of human Caspase-1 with (3S,6S,10aS)-N-((2S,3S)-2-hydroxy-5-oxotetrahydrofuran-3-yl)-6-(isoquinoline-1-carboxamido)-5-oxodecahydropyrrolo[1,2-a]azocine-3-carboxamide (PGE-3935199)

• PDB DOI: https://doi.org/10.2210/pdb5MTK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-01-09 Released: 2018-02-28 
• Deposition Author(s): Brethon, A., Chantalat, L., Christin, O., Clary, L., Fournier, J.F., Gastreich, M., Harris, C., Pascau, J., Isabet, T., Rodeschin, V., Thoreau, E., Roche, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free: 
  0.299 (Depositor), 0.370 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.300 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Literature

Playing against the odds: scaffold hopping from 3D-fragments

Brethon, A., Chantalat, L., Christin, O., Clary, L., Fournier, J.F., Gastreich, M., Harris, C., Pascau, J., Isabet, T., Rodeschin, V., Thoreau, E., Roche, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 30.87 kDa 
• Atom Count: 2,069 
• Modelled Residue Count: 253 
• Deposited Residue Count: 268 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-1	A	179	Homo sapiens	Mutation(s): 0  Gene Names: CASP1, IL1BC, IL1BCE EC: 3.4.22.36
UniProt & NIH Common Fund Data Resources
Find proteins for P29466 (Homo sapiens) Explore P29466  Go to UniProtKB:  P29466
PHAROS:  P29466 GTEx:  ENSG00000137752

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-1	B	89	Homo sapiens	Mutation(s): 0  Gene Names: CASP1, IL1BC, IL1BCE EC: 3.4.22.36
UniProt & NIH Common Fund Data Resources
Find proteins for P29466 (Homo sapiens) Explore P29466  Go to UniProtKB:  P29466
PHAROS:  P29466 GTEx:  ENSG00000137752

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N7N	C [auth A]	(3~{S})-3-[[(3~{S},6~{S},10~{a}~{S})-6-(isoquinolin-1-ylcarbonylamino)-5-oxidanylidene-2,3,6,7,8,9,10,10~{a}-octahydro-1~{H}-pyrrolo[1,2-a]azocin-3-yl]carbonylamino]-4-oxidanyl-butanoic acid C25 H30 N4 O6 AVBDMGZDLMBHDP-ZULIPRJHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.53 Å
• R-Value Free:  0.299 (Depositor), 0.370 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.300 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.589	α = 90
b = 64.589	β = 90
c = 161.102	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
SCALA	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-02-28 
Deposition Author(s): Brethon, A., Chantalat, L., Christin, O., Clary, L., Fournier, J.F., Gastreich, M., Harris, C., Pascau, J., Isabet, T., Rodeschin, V., Thoreau, E., Roche, D.

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Structure summary