4OYI

Human solAC Complexed with (4-Amino-furazan-3-yl)-phenyl-methanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of human soluble adenylate cyclase reveals a distinct, highly flexible allosteric bicarbonate binding pocket.

Saalau-Bethell, S.M.Berdini, V.Cleasby, A.Congreve, M.Coyle, J.E.Lock, V.Murray, C.W.O'Brien, M.A.Rich, S.J.Sambrook, T.Vinkovic, M.Yon, J.R.Jhoti, H.

(2014) Chemmedchem 9: 823-832

  • DOI: 10.1002/cmdc.201300480
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Soluble adenylate cyclases catalyse the synthesis of the second messenger cAMP through the cyclisation of ATP and are the only known enzymes to be directly activated by bicarbonate. Here, we report the first crystal structure of the human enzyme that ...

    Soluble adenylate cyclases catalyse the synthesis of the second messenger cAMP through the cyclisation of ATP and are the only known enzymes to be directly activated by bicarbonate. Here, we report the first crystal structure of the human enzyme that reveals a pseudosymmetrical arrangement of two catalytic domains to produce a single competent active site and a novel discrete bicarbonate binding pocket. Crystal structures of the apo protein, the protein in complex with α,β-methylene adenosine 5'-triphosphate (AMPCPP) and calcium, with the allosteric activator bicarbonate, and also with a number of inhibitors identified using fragment screening, all show a flexible active site that undergoes significant conformational changes on binding of ligands. The resulting nanomolar-potent inhibitors that were developed bind at both the substrate binding pocket and the allosteric site, and can be used as chemical probes to further elucidate the function of this protein.


    Organizational Affiliation

    Astex Pharmaceuticals, Cambridge Science Park, Cambridge, CB4 0QA (UK).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Adenylate cyclase type 10
A
470Homo sapiensMutation(s): 0 
Gene Names: ADCY10 (SAC)
EC: 4.6.1.1
Find proteins for Q96PN6 (Homo sapiens)
Go to Gene View: ADCY10
Go to UniProtKB:  Q96PN6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
1VK
Query on 1VK

Download SDF File 
Download CCD File 
A
(4-azanyl-1,2,5-oxadiazol-3-yl)-phenyl-methanone
C9 H7 N3 O2
FSUWRFXTSWSYPV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
ACE
Query on ACE
A
NON-POLYMERC2 H4 O

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1VKIC50: 19000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.170 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 98.995α = 90.00
b = 98.995β = 90.00
c = 97.744γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-02-12 
  • Released Date: 2014-04-02 
  • Deposition Author(s): Vinkovic, M.

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-10-01
    Type: Database references