6O1S | pdb_00006o1s

Structure of human plasma kallikrein protease domain with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.201 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structures of full-length plasma kallikrein bound to highly specific inhibitors describe a new mode of targeted inhibition.

Partridge, J.R.Choy, R.M.Silva-Garcia, A.Yu, C.Li, Z.Sham, H.Metcalf, B.

(2019) J Struct Biol 206: 170-182

  • DOI: https://doi.org/10.1016/j.jsb.2019.03.001
  • Primary Citation Related Structures: 
    6BFP, 6O1G, 6O1S

  • PubMed Abstract: 

    Plasma kallikrein (pKal) is a serine protease responsible for cleaving high-molecular-weight kininogen to produce the pro-inflammatory peptide, bradykinin. Unregulated pKal activity can lead to hereditary angioedema (HAE) following excess bradykinin release. HAE attacks can lead to a compromised airway that can be life threatening. As there are limited agents for prophylaxis of HAE attacks, there is a high unmet need for a therapeutic agent for regulating pKal with a high degree of specificity. Here we present crystal structures of both full-length and the protease domain of pKal, bound to two very distinct classes of small-molecule inhibitors: compound 1, and BCX4161. Both inhibitors demonstrate low nM inhibitory potency for pKal and varying specificity for related serine proteases. Compound 1 utilizes a surprising mode of interaction and upon binding results in a rearrangement of the binding pocket. Co-crystal structures of pKal describes why this class of small-molecule inhibitor is potent. Lack of conservation in surrounding residues explains the ∼10,000-fold specificity over structurally similar proteases, as shown by in vitro protease inhibition data. Structural information, combined with biochemical and enzymatic analyses, provides a novel scaffold for the design of targeted oral small molecule inhibitors of pKal for treatment of HAE and other diseases resulting from unregulated plasma kallikrein activity.


  • Organizational Affiliation
    • Global Blood Therapeutics, South San Francisco, CA 94080, United States. Electronic address: jpartridge@gbt.com.

Macromolecule Content 

  • Total Structure Weight: 30 kDa 
  • Atom Count: 2,158 
  • Modeled Residue Count: 239 
  • Deposited Residue Count: 263 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Plasma kallikreinA [auth E]263Homo sapiensMutation(s): 4 
Gene Names: KLKB1KLK3
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7SD
(Subject of Investigation/LOI)

Query on 7SD



Download:Ideal Coordinates CCD File
D [auth E]N-[(6-amino-2,4-dimethylpyridin-3-yl)methyl]-1-({4-[(1H-pyrazol-1-yl)methyl]phenyl}methyl)-1H-pyrazole-4-carboxamide
C23 H25 N7 O
OINOKQVNBGAIMA-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
B [auth E]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
C [auth E]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
7SD BindingDB:  6O1S IC50: min: 0.2, max: 2.4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.201 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.685α = 90
b = 57.45β = 90
c = 86.215γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-15
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary