3RXD

Crystal structure of Trypsin complexed with (3-methoxyphenyl)methanamine

• PDB DOI: https://doi.org/10.2210/pdb3RXD/pdb

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


• Deposited: 2011-05-10 Released: 2011-08-24 
• Deposition Author(s): Yamane, J., Yao, M., Zhou, Y., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.189 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 

Starting Model: experimental

Literature

In-crystal affinity ranking of fragment hit compounds reveals a relationship with their inhibitory activities

Yamane, J., Yao, M., Zhou, Y., Hiramatsu, Y., Fujiwara, K., Yamaguchi, T., Yamaguchi, H., Togame, H., Tsujishita, H., Takemoto, H., Tanaka, I.

(2011) J Appl Crystallogr 44: 798-804

• DOI: https://doi.org/10.1107/S0021889811017717

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 23.84 kDa 
• Atom Count: 1,970 
• 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
SZ4	G [auth A]	1-(3-methoxyphenyl)methanamine C8 H11 N O GRRIMVWABNHKBX-UHFFFAOYSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	E [auth A], F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SZ4	PDBBind:  3RXD	IC50: 1.88e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.189 
• R-Value Work: 0.161 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.285	α = 90
b = 58.243	β = 90
c = 66.755	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-24 
Deposition Author(s): Yamane, J., Yao, M., Zhou, Y., Tanaka, I.

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary