5TJX

Structure of human plasma kallikrein

Experimental Data Snapshot

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

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


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

  • DOI: 10.1021/acsmedchemlett.6b00384
  • Primary Citation of 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 ...

    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.

    Organizational Affiliation: 

    Pharmaron Xi'an Co. , Xi'an, Shaanxi 710018, China.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plasma kallikreinA263Homo sapiensMutation(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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03952
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GBT
Query on GBT
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GBT BindingDB:  5TJX IC50: min: 2, max: 4.8 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.66α = 90
b = 59.62β = 90
c = 77.11γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references