5TJX | pdb_00005tjx

Structure of human plasma kallikrein

• PDB DOI: https://doi.org/10.2210/pdb5TJX/pdb

• Classification: Hydrolase/Hydrolase Inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2016-10-05 Released: 2016-12-21 
• Deposition Author(s): Partridge, J.R., Choy, R.M., Li, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 
  0.184 (Depositor) 
• R-Value Work: 
  0.163 (Depositor) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Structure-Guided Design of Novel, Potent, and Selective Macrocyclic Plasma Kallikrein Inhibitors.

Li, Z., Partridge, J., Silva-Garcia, A., Rademacher, P., Betz, A., Xu, Q., Sham, H., Hu, Y., Shan, Y., Liu, B., Zhang, Y., Shi, H., Xu, Q., Ma, X., Zhang, L.

(2017) ACS Med Chem Lett 8: 185-190

• PubMed: 28197309 
• DOI: https://doi.org/10.1021/acsmedchemlett.6b00384
• Primary Citation Related Structures: 
  5TJX


• PubMed Abstract: 
  

  A series of macrocyclic analogues were designed and synthesized based on the cocrystal structure of small molecule plasma kallikrein (pKal) inhibitor, 2 , with the pKal protease domain. This led to the discovery of a potent macrocyclic pKal inhibitor 29 , with an IC ₅₀ of 2 nM for one olefinic isomer and 42.3 nM for the other olefinic isomer.

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Organizational Affiliation: 
• Global Blood Therapeutics , South San Francisco, California 94080, United States.
Pharmaron Xi'an Co. , Xi'an, Shaanxi 710018, China.

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: 30.14 kDa 
• Atom Count: 2,244 
• Modeled Residue Count: 231 
• Deposited Residue Count: 263 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasma kallikrein	A	263	Homo sapiens	Mutation(s): 4  Gene Names: KLKB1, KLK3 EC: 3.4.21.34
UniProt & NIH Common Fund Data Resources
Find proteins for P03952 (Homo sapiens) Explore P03952  Go to UniProtKB:  P03952
PHAROS:  P03952 GTEx:  ENSG00000164344

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GBT	B [auth A]	(8E)-3-amino-1-methyl-15-[(1H-pyrazol-1-yl)methyl]-7,10,11,12,24,25-hexahydro-6H,18H,23H-19,22-(metheno)pyrido[4,3-j][1,9,13,17,18]benzodioxatriazacyclohenicosin-23-one C29 H33 N7 O3 ZVYLYYBRLJOHMS-DUXPYHPUSA-N
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
GBT	BindingDB:  5TJX	IC50: 2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free:  0.184 (Depositor) 
• R-Value Work:  0.163 (Depositor) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.66	α = 90
b = 59.62	β = 90
c = 77.11	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-21 
Deposition Author(s): Partridge, J.R., Choy, R.M., Li, Z.

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2017-03-01
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary