9D4D | pdb_00009d4d

Crystal structure of the catalytic region of human MASP-2 with specific inhibitor Compound S3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.251 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.200 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Small molecule inhibitors of mannan-binding lectin-associated serine Proteases-2 and-3.

Nakhla, M.C.Comita, J.Shapiro, A.B.Moussa, S.H.Chen, A.Eyermann, C.J.O'Donnell, J.P.Miller, A.A.Granger, B.A.

(2025) Eur J Med Chem 289: 117238-117238

  • DOI: https://doi.org/10.1016/j.ejmech.2025.117238
  • Primary Citation of Related Structures:  
    9D17, 9D3Y, 9D40, 9D4D

  • PubMed Abstract: 

    The complement system of innate immunity recognizes, opsonizes, and kills invading pathogens and damaged cells, and stimulates an inflammatory response. Inappropriate or excessive complement activity is associated with a wide variety of pathological conditions, and several drugs targeting complement components have been approved. Here we describe the discovery and structure-activity relationships of a novel class of 2-aminoimidazole-containing inhibitors of mannan-binding lectin-associated serine proteases -2 and -3 (MASP-2 and MASP-3), essential enzymes for activation of the lectin and alternative pathways of complement, respectively. With a high degree of target selectivity and favorable in vitro pharmacological properties, this inhibitor series has the potential to be developed as treatments for numerous diseases and pathological conditions.


  • Organizational Affiliation

    Innoviva Specialty Therapeutics, Inc., Waltham, MA, 02451, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mannan-binding lectin serine protease 2 B chain324Homo sapiensMutation(s): 0 
Gene Names: MASP2
EC: 3.4.21.104
UniProt & NIH Common Fund Data Resources
Find proteins for O00187 (Homo sapiens)
Explore O00187 
Go to UniProtKB:  O00187
PHAROS:  O00187
GTEx:  ENSG00000009724 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00187
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A10 (Subject of Investigation/LOI)
Query on A1A10

Download Ideal Coordinates CCD File 
I [auth A]2-(2-amino-1H-1,3-benzimidazol-4-yl)-N-{4-[(pyridin-4-yl)methyl]phenyl}acetamide
C21 H19 N5 O
AGVCSHCLKHPSSZ-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.251 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.200 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.65α = 90
b = 41.11β = 98.22
c = 103.13γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-16
    Type: Initial release