9D17 | pdb_00009d17

Crystal structure of the catalytic region of human MASP-2 with specific inhibitor Compound S1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.243 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.201 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9D17

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 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.

Macromolecule Content 

  • Total Structure Weight: 36.08 kDa 
  • Atom Count: 2,548 
  • Modeled Residue Count: 319 
  • Deposited Residue Count: 324 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A1X
(Subject of Investigation/LOI)

Query on A1A1X



Download:Ideal Coordinates CCD File
B [auth A]2-(2-amino-1H-1,3-benzimidazol-1-yl)-N-(5-ethylpyridin-2-yl)acetamide
C16 H17 N5 O
DDGFJCBIYRJVAU-UHFFFAOYSA-N
GOL

Query on GOL



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

Query on DMS



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.243 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.201 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.84α = 90
b = 40.81β = 97.52
c = 101.5γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



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