8B75

CRYSTAL STRUCTURE OF HUMAN SOLUBLE ADENYLYL CYCLASE IN COMPLEX WITH THE INHIBITOR TDI-011861

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2022-09-28 Released: 2023-03-29 
  • Deposition Author(s): Steegborn, C., Kehr, M.
  • Funding Organization(s): German Research Foundation (DFG), National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Design, Synthesis, and Pharmacological Evaluation of Second-Generation Soluble Adenylyl Cyclase (sAC, ADCY10) Inhibitors with Slow Dissociation Rates.

Miller, M.Rossetti, T.Ferreira, J.Ghanem, L.Balbach, M.Kaur, N.Levin, L.R.Buck, J.Kehr, M.Coquille, S.van den Heuvel, J.Steegborn, C.Fushimi, M.Finkin-Groner, E.Myers, R.W.Kargman, S.Liverton, N.J.Huggins, D.J.Meinke, P.T.

(2022) J Med Chem 65: 15208-15226

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01133
  • Primary Citation of Related Structures:  
    8B75

  • PubMed Abstract: 

    Soluble adenylyl cyclase (sAC: ADCY10) is an enzyme involved in intracellular signaling. Inhibition of sAC has potential therapeutic utility in a number of areas. For example, sAC is integral to successful male fertility: sAC activation is required for sperm motility and ability to undergo the acrosome reaction, two processes central to oocyte fertilization. Pharmacologic evaluation of existing sAC inhibitors for utility as on-demand, nonhormonal male contraceptives suggested that both high intrinsic potency, fast on and slow dissociation rates are essential design elements for successful male contraceptive applications. During the course of the medicinal chemistry campaign described here, we identified sAC inhibitors that fulfill these criteria and are suitable for in vivo evaluation of diverse sAC pharmacology.


  • Organizational Affiliation

    Tri-Institutional Therapeutics Discovery Institute, New York, New York 10021, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenylate cyclase type 10475Homo sapiensMutation(s): 0 
Gene Names: ADCY10SAC
EC: 4.6.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PN6 (Homo sapiens)
Explore Q96PN6 
Go to UniProtKB:  Q96PN6
PHAROS:  Q96PN6
GTEx:  ENSG00000143199 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96PN6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PJU (Subject of Investigation/LOI)
Query on PJU

Download Ideal Coordinates CCD File 
B [auth A][(3~{R})-4-[2-[2-[[3-(2-azanyl-6-chloranyl-pyrimidin-4-yl)-1-[bis(fluoranyl)methyl]pyrazol-4-yl]methyl]phenoxy]ethyl]morpholin-3-yl]methanol
C22 H25 Cl F2 N6 O3
XVGSKZXXLKUEIO-MRXNPFEDSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.203 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.131α = 90
b = 100.131β = 90
c = 97.889γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description