4PID | pdb_00004pid

Crystal structure of human adenovirus 2 protease with a weak pyrimidine nitrile inhibitor

PDB DOI: https://doi.org/10.2210/pdb4PID/pdb

Classification: Hydrolase/Hydrolase Inhibitor
Organism(s): Human adenovirus 2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-05-08 Released: 2014-09-10
Deposition Author(s): Mac Sweeney, A., Grosche, P., Ellis, D., Combrink, K., Erbel, P., Hughes, N., Sirockin, F., Melkko, S., Bernardi, A., Ramage, P., Jarousse, N., Altmann, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.189 (Depositor), 0.187 (DCC)
R-Value Work:
0.165 (Depositor), 0.163 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Discovery and structure-based optimization of adenain inhibitors.

Mac Sweeney, A., Grosche, P., Ellis, D., Combrink, K., Erbel, P., Hughes, N., Sirockin, F., Melkko, S., Bernardi, A., Ramage, P., Jarousse, N., Altmann, E.

(2014) ACS Med Chem Lett 5: 937-941

PubMed: 25147618 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/ml500224t
Primary Citation Related Structures:
4PID, 4PIE, 4PIQ, 4PIS

PubMed Abstract:
The cysteine protease adenain is the essential protease of adenovirus and, as such, represents a promising target for the treatment of ocular and other adenoviral infections. Through a concise two-pronged hit discovery approach we identified tetrapeptide nitrile 1 and pyrimidine nitrile 2 as complementary starting points for adenain inhibition. These hits enabled the first high-resolution X-ray cocrystal structures of adenain with inhibitors bound and revealed the binding mode of 1 and 2. The screening hits were optimized by a structure-guided medicinal chemistry strategy into low nanomolar drug-like inhibitors of adenain.

Organizational Affiliation

Novartis Institute for Biomedical Research , Novartis Campus, CH-4002 Basel, Switzerland.

Macromolecule Content

Total Structure Weight: 24.77 kDa
Atom Count: 1,918
Modeled Residue Count: 215
Deposited Residue Count: 215
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A	204	Human adenovirus 2	Mutation(s): 0 Gene Names: L3 EC: 3.4.22.39
UniProt
Find proteins for P03252 (Human adenovirus C serotype 2) Explore P03252 Go to UniProtKB: P03252
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03252
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pre-protein VI	B	11	Human adenovirus 2	Mutation(s): 0
UniProt
Find proteins for P03274 (Human adenovirus C serotype 2) Explore P03274 Go to UniProtKB: P03274
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03274
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2UQ Query on 2UQ Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	N-benzyl-2-[(Z)-iminomethyl]pyrimidine-5-carboxamide C₁₃ H₁₂ N₄ O LOHVEJATQLMRBB-MKMNVTDBSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.189 (Depositor), 0.187 (DCC)
R-Value Work: 0.165 (Depositor), 0.163 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.783	α = 90
b = 112.783	β = 90
c = 50.347	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-09-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-10
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Other, Refinement description, Source and taxonomy
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary