6T7P

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 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

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Ligand Structure Quality Assessment 


This is version 1.1 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: 10.1021/acs.jmedchem.0c00279
  • Primary Citation of 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 ...

    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, Cambridge, Massachusetts 02139, United States.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plasma kallikreinA242Homo sapiensMutation(s): 0 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / 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		 Ligand Interaction
GSH
Query on GSH
Download Ideal Coordinates CCD File 
B [auth A]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
M [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
N [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
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		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MU8 Binding MOAD:  6T7P Ki: 970 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 
  • 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

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Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2019-10-22 
  • 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