6T7P | pdb_00006t7p

human plasmakallikrein protease domain in complex with active site directed inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6T7P

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Design and Preclinical Characterization of Selective and Orally Bioavailable Factor XIa Inhibitors: Demonstrating the Power of an Integrated S1 Protease Family Approach.

Lorthiois, E.Roache, J.Barnes-Seeman, D.Altmann, E.Hassiepen, U.Turner, G.Duvadie, R.Hornak, V.Karki, R.G.Schiering, N.Weihofen, W.A.Perruccio, F.Calhoun, A.Fazal, T.Dedic, D.Durand, C.Dussauge, S.Fettis, K.Tritsch, F.Dentel, C.Druet, A.Liu, D.Kirman, L.Lachal, J.Namoto, K.Bevan, D.Mo, R.Monnet, G.Muller, L.Zessis, R.Huang, X.Lindsley, L.Currie, T.Chiu, Y.H.Fridrich, C.Delgado, P.Wang, S.Hollis-Symynkywicz, M.Berghausen, J.Williams, E.Liu, H.Liang, G.Kim, H.Hoffmann, P.Hein, A.Ramage, P.D'Arcy, A.Harlfinger, S.Renatus, M.Ruedisser, S.Feldman, D.Elliott, J.Sedrani, R.Maibaum, J.Adams, C.M.

(2020) J Med Chem 63: 8088-8113

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00279
  • Primary Citation Related Structures: 
    6T7P, 6TS4, 6TS5, 6TS6, 6TS7, 6USY

  • PubMed Abstract: 

    The serine protease factor XI (FXI) is a prominent drug target as it holds promise to deliver efficacious anticoagulation without an enhanced risk of major bleeds. Several efforts have been described targeting the active form of the enzyme, FXIa. Herein, we disclose our efforts to identify potent, selective, and orally bioavailable inhibitors of FXIa. Compound 1 , identified from a diverse library of internal serine protease inhibitors, was originally designed as a complement factor D inhibitor and exhibited submicromolar FXIa activity and an encouraging absorption, distribution, metabolism, and excretion (ADME) profile while being devoid of a peptidomimetic architecture. Optimization of interactions in the S1, S1β, and S1' pockets of FXIa through a combination of structure-based drug design and traditional medicinal chemistry led to the discovery of compound 23 with subnanomolar potency on FXIa, enhanced selectivity over other coagulation proteases, and a preclinical pharmacokinetics (PK) profile consistent with bid dosing in patients.


  • Organizational Affiliation
    • Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 28.92 kDa 
  • Atom Count: 2,447 
  • Modeled Residue Count: 237 
  • Deposited Residue Count: 242 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Plasma kallikrein242Homo sapiensMutation(s): 0 
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
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MU8
(Subject of Investigation/LOI)

Query on MU8



Download:Ideal Coordinates CCD File
O [auth A](2~{S},4~{R})-1-[[(3~{S})-3-azanyl-2,3-dihydro-1-benzofuran-6-yl]carbonyl]-~{N}-(3-chlorophenyl)-4-phenyl-pyrrolidine-2-carboxamide
C26 H24 Cl N3 O3
WXCDYJQWHUGJRV-NMNUPHIUSA-N
GSH

Query on GSH



Download:Ideal Coordinates CCD File
B [auth A]Glutathione
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
M [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
N [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS

Query on DMS



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.155 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.1α = 90
b = 59.15β = 90
c = 86.72γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-07-08 
  • Deposition Author(s): Renatus, M.

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-08-26
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description