3RXM

Crystal structure of Trypsin complexed with [2-(2-thienyl)thiazol-4-yl]methanamine

PDB DOI: https://doi.org/10.2210/pdb3RXM/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.185
R-Value Work: 0.160
R-Value Observed: 0.161

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 24.06 kDa
Atom Count: 1,996
Modelled Residue Count: 223
Deposited Residue Count: 223
Unique protein chains: 1

Macromolecules

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(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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SW1 Query on SW1 Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	1-[2-(thiophen-2-yl)-1,3-thiazol-4-yl]methanamine C₈ H₈ N₂ S₂ VZBJIPJKJKKWPH-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
SW1	PDBBind: 3RXM	IC50: 2.32e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.185
R-Value Work: 0.160
R-Value Observed: 0.161
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.405	α = 90
b = 58.172	β = 90
c = 66.895	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-24

Deposition Author(s):

Revision History (Full details and data files)

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: 2024-10-30
Changes: Structure summary

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Help and Resources

3RXM

Crystal structure of Trypsin complexed with [2-(2-thienyl)thiazol-4-yl]methanamine

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)