7OVD | pdb_00007ovd

Human soluble adenylyl cyclase in complex with the inhibitor TDI10229

PDB DOI: https://doi.org/10.2210/pdb7OVD/pdb

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

Deposited: 2021-06-14 Released: 2021-10-06
Deposition Author(s): Steegborn, C., Quast, J.
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: 2.20 Å
R-Value Free:
0.243 (Depositor), 0.247 (DCC)
R-Value Work:
0.199 (Depositor), 0.201 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of TDI-10229: A Potent and Orally Bioavailable Inhibitor of Soluble Adenylyl Cyclase (sAC, ADCY10).

Fushimi, M., Buck, H., Balbach, M., Gorovyy, A., Ferreira, J., Rossetti, T., Kaur, N., Levin, L.R., Buck, J., Quast, J., van den Heuvel, J., Steegborn, C., Finkin-Groner, E., Kargman, S., Michino, M., Foley, M.A., Miller, M., Liverton, N.J., Huggins, D.J., Meinke, P.T.

(2021) ACS Med Chem Lett 12: 1283-1287

PubMed: 34413957 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.1c00273
Primary Citation Related Structures:
7OVD

PubMed Abstract:
Soluble adenylyl cyclase (sAC) has gained attention as a potential therapeutic target given the role of this enzyme in intracellular signaling. We describe successful efforts to design improved sAC inhibitors amenable for in vivo interrogation of sAC inhibition to assess its potential therapeutic applications. This work culminated in the identification of TDI-10229 ( 12 ), which displays nanomolar inhibition of sAC in both biochemical and cellular assays and exhibits mouse pharmacokinetic properties sufficient to warrant its use as an in vivo tool compound.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 55.5 kDa
Atom Count: 3,744
Modeled Residue Count: 449
Deposited Residue Count: 475
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96PN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1S2 (Subject of Investigation/LOI) Query on 1S2 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	4-chloranyl-6-[1,5-dimethyl-4-(phenylmethyl)pyrazol-3-yl]pyrimidin-2-amine C₁₆ H₁₆ Cl N₅ VSMTYSWGHKYXOF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain L [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain L [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain L [auth A]	D [auth A], E [auth A], F [auth A], L [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain L [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	G [auth A] H [auth A] K [auth A] M [auth A] N [auth A] G [auth A], H [auth A], K [auth A], M [auth A], N [auth A], O [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth A] MOL2 format, chain C [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth A] mmCIF format, chain C [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth A]	C [auth A], I [auth A], J [auth A], P [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth A] Interactions & Density Focus chain C [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.243 (Depositor), 0.247 (DCC)
R-Value Work: 0.199 (Depositor), 0.201 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.177	α = 90
b = 99.177	β = 90
c = 99.593	γ = 120

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

Steegborn, C.

Quast, J.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	STE1701/11
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	P50 HD100549