6O1G | pdb_00006o1g

Full length human plasma kallikrein with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.240 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6O1G

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: 72.31 kDa 
  • Atom Count: 4,796 
  • Modeled Residue Count: 588 
  • Deposited Residue Count: 638 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Plasma kallikrein638Homo sapiensMutation(s): 0 
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
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7SD
(Subject of Investigation/LOI)

Query on 7SD



Download:Ideal Coordinates CCD File
D [auth A]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
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
7SD BindingDB:  6O1G IC50: min: 0.2, max: 2.4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.240 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.97α = 90
b = 121.92β = 105.79
c = 65.89γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Structure summary