5IV4 | pdb_00005iv4

Crystal structure of the human soluble adenylyl cyclase in complex with the allosteric inhibitor LRE1

• PDB DOI: https://doi.org/10.2210/pdb5IV4/pdb

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


• Deposited: 2016-03-18 Released: 2016-08-17 
• Deposition Author(s): Kleinboelting, S., Steegborn, C.
• Funding Organization(s): German Research Foundation

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.206 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Literature

Discovery of LRE1 as a specific and allosteric inhibitor of soluble adenylyl cyclase.

Ramos-Espiritu, L., Kleinboelting, S., Navarrete, F.A., Alvau, A., Visconti, P.E., Valsecchi, F., Starkov, A., Manfredi, G., Buck, H., Adura, C., Zippin, J.H., van den Heuvel, J., Glickman, J.F., Steegborn, C., Levin, L.R., Buck, J.

(2016) Nat Chem Biol 12: 838-844

• PubMed: 27547922 
• DOI: https://doi.org/10.1038/nchembio.2151
• Primary Citation Related Structures: 
  5IV3, 5IV4


• PubMed Abstract: 
  

  The prototypical second messenger cAMP regulates a wide variety of physiological processes. It can simultaneously mediate diverse functions by acting locally in independently regulated microdomains. In mammalian cells, two types of adenylyl cyclase generate cAMP: G-protein-regulated transmembrane adenylyl cyclases and bicarbonate-, calcium- and ATP-regulated soluble adenylyl cyclase (sAC). Because each type of cyclase regulates distinct microdomains, methods to distinguish between them are needed to understand cAMP signaling. We developed a mass-spectrometry-based adenylyl cyclase assay, which we used to identify a new sAC-specific inhibitor, LRE1. LRE1 bound to the bicarbonate activator binding site and inhibited sAC via a unique allosteric mechanism. LRE1 prevented sAC-dependent processes in cellular and physiological systems, and it will facilitate exploration of the therapeutic potential of sAC inhibition.

---

Organizational Affiliation: 
• Department of Pharmacology, Weill Cornell Medical College, New York, New York, USA.
The High-Throughput Screening and Spectroscopy Resource Center, The Rockefeller University, New York, New York, USA.
Department of Biochemistry, University of Bayreuth, Bayreuth, Germany.
Department of Veterinary and Animal Science, University of Massachusetts, Amherst, Massachusetts, USA.
Brain and Mind Research Institute, Weill Cornell Medical College, New York, New York, USA.
Department of Dermatology, Weill Cornell Medical College, New York, New York, USA.
Helmholtz Zentrum fur Infektionsforschung, Braunschweig, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 55.53 kDa 
• Atom Count: 4,164 
• Modeled Residue Count: 461 
• Deposited Residue Count: 475 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate cyclase type 10	A	475	Homo sapiens	Mutation(s): 0  Gene Names: ADCY10, SAC 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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LRI	B [auth A]	6-chloro-N~4~-cyclopropyl-N~4~-[(thiophen-2-yl)methyl]pyrimidine-2,4-diamine C12 H13 Cl N4 S PDWZXKSZLRVSEH-UHFFFAOYSA-N
PEG	O [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	P [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	J [auth A], K [auth A], L [auth A], M [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	N [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
LRI	BindingDB:  5IV4	IC50: min: 1500, max: 6300 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.206 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.298	α = 90
b = 99.298	β = 90
c = 99.386	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Coot	model building
MOLREP	phasing
XSCALE	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): Kleinboelting, S., Steegborn, C.

---

Funding Organization	Location	Grant Number
German Research Foundation	Germany	STE1701/11

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2016-08-31
  Changes: Database references
• Version 1.2: 2016-09-28
  Changes: Database references
• Version 1.3: 2022-11-30
  Changes: Author supporting evidence, Database references, Source and taxonomy, Structure summary
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary