Protein profile

PA2499

deaminase

Genome: NC_002516.2

Gene: PA2499 Structure source: AlphaFold UniProt Q9I0Y3

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Amino acids 151

Annotations 8

Features 12

PDB binders 12

Druggability 0.586

Overview

Basic information about this protein and its source genome.

Accession: PA2499
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA2499
Status: annotated
Amino acids: 151
Structure source: AlphaFold

GO:0047974 Catalysis of the reaction: guanosine + H2O + H+ = xanthosine + NH4+. GO:0052717 Catalysis of the reaction: adenosine34 in tRNA + H2O + H+ = inosine34 in tRNA + NH4+. GO:0008270 Binding to a zinc ion (Zn). GO:0006152 The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside). GO:0002100 The process in which an adenosine at position 34 of a tRNA is post-transcriptionally converted to inosine. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 30.081
Human E-value: 9.44e-12
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.586

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

GO:0047974 Catalysis of the reaction: guanosine + H2O + H+ = xanthosine + NH4+.
GO:0052717 Catalysis of the reaction: adenosine34 in tRNA + H2O + H+ = inosine34 in tRNA + NH4+.
GO:0008270 Binding to a zinc ion (Zn).
GO:0006152 The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
GO:0002100 The process in which an adenosine at position 34 of a tRNA is post-transcriptionally converted to inosine. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0008251 Catalysis of the reaction: adenosine + H2O = inosine + NH4+, in a tRNA molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
1	147	FunFam	G3DSA:3.40.140.10:FF:000051	Nucleoside deaminase
2	127	SUPERFAMILY	SSF53927	Cytidine deaminase-like
2	127	InterPro	IPR016193	Cytidine deaminase-like
1	106	Pfam	PF14437	MafB19-like deaminase
1	106	InterPro	IPR028883	tRNA-specific adenosine deaminase
1	112	ProSiteProfiles	PS51747	Cytidine and deoxycytidylate deaminases domain profile.
1	112	InterPro	IPR002125	Cytidine and deoxycytidylate deaminase domain
1	151	Gene3D	G3DSA:3.40.140.10	Cytidine Deaminase, domain 2
7	110	CDD	cd01285	nucleoside_deaminase
2	113	PANTHER	PTHR11079	CYTOSINE DEAMINASE FAMILY MEMBER
52	89	ProSitePatterns	PS00903	Cytidine and deoxycytidylate deaminases zinc-binding region signature.
52	89	InterPro	IPR016192	APOBEC/CMP deaminase, zinc-binding

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA2499	AlphaFold	—	—	full sequence	—	Viewing

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.586

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

62 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
5AZ	5XKP	A0QY90	112.1 Da LogP -1.25 TPSA 84.7	✓ Ro5	✓ Clean	`C1=NC(=O)NC(=N1)N`
6AM	5XKQ	A0QY90	127.1 Da LogP -1.26 TPSA 110.9	✓ Ro5	✓ Clean	`c1(nc(nc(n1)O)N)N`
6AP	4LCP	Q82Y41	150.1 Da LogP -0.48 TPSA 106.5	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)c(nc(n2)N)N`
9MG	4LC5	Q82Y41	165.2 Da LogP -0.35 TPSA 89.8	✓ Ro5	✓ Clean	`Cn1cnc2c1nc(nc2O)N`
AZG	4HRQ	Q82Y41	152.1 Da LogP -0.96 TPSA 113.6	✓ Ro5	✓ Clean	`c12c(nc(nc1O)N)nn[nH]2`
BZE	5XKR	A0QY90	187.2 Da LogP 0.70 TPSA 90.7	✓ Ro5	✓ Clean	`c1ccc(cc1)c2nc(nc(n2)N)N`
CAC	5XKO	A0QY90	137.0 Da LogP -0.52 TPSA 40.1	✓ Ro5	✓ Clean	`C[As](=O)(C)[O-]`
CTN	4LD2	Q82Y41	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`
CYT	4LD4	Q82Y41	111.1 Da LogP -0.65 TPSA 71.8	✓ Ro5	✓ Clean	`C1=C(NC(=O)N=C1)N`
DUC	1UAQ	Q12178	114.1 Da LogP -0.78 TPSA 58.2	✓ Ro5	✓ Clean	`C1CNC(=O)NC1=O`
GNG	4LCN	Q82Y41	267.2 Da LogP -1.66 TPSA 139.3	✓ Ro5	✓ Clean	`c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO)O)NC(=NC2=O)N`
HPY	1P6O	Q12178	114.1 Da LogP -0.87 TPSA 61.4	✓ Ro5	✓ Clean	`C1=CNC(=O)N[C@H]1O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1078621	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)n1`
ZINC12336757	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c(=O)n1`
ZINC12336758	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c(=O)n1`
ZINC16969357	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC2583632	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)n1`
ZINC3795098	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c(=O)…`
ZINC3830623	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c(=O)n1`
ZINC3830624	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c(=O)…`
ZINC3978018	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c(=O)n1`
ZINC6091575	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC6234828	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC6524892	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC895248	1.000	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@@H]2O)c(=O)n1`
ZINC1718514	0.900	248.3 Da LogP 2.79 TPSA 64.7	✓ Ro5	✓ Clean	`Nc1nc(-c2ccccc2)nc(-c2ccccc2)n1`
ZINC34085615	0.829	242.2 Da LogP -2.60 TPSA 136.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2N)c(=O)n1`
ZINC13546396	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2F)c(=O)n1`
ZINC16952044	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@H]2F)c(=O)n1`
ZINC17174505	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2F)c(=O…`
ZINC17174506	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2F)c(=O)…`
ZINC2522524	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@@H]2F)c(=O)n1`
ZINC3817231	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2F)c(=O)n1`
ZINC57331	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2F)c(=O)…`
ZINC5758597	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2F)c(=O)n1`
ZINC5758598	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2F)c(=O)…`
ZINC59201305	0.810	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2F)c(=O)n1`
ZINC6524890	0.786	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](F)[C@H]2O)c(=O)n1`
ZINC85475812	0.786	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](F)[C@H]2O)c(=O)n1`
ZINC13546402	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC14953681	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](n2ccc(N)nc2=O)O[C@H](CO)[C@H]1O`
ZINC257373216	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](O)[C@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC35635704	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@H](O)[C@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC3806784	0.756	252.2 Da LogP -1.78 TPSA 134.4	✓ Ro5	✓ Clean	`N#C[C@H]1[C@H](O)[C@@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC38599713	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC4556822	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](n2ccc(N)nc2=O)O[C@@H](CO)[C@H]1O`
ZINC4556823	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@@H](n2ccc(N)nc2=O)O[C@@H](CO)[C@H]1O`
ZINC4556824	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@@H](O)[C@H](CO)O[C@@H]1n1ccc(N)nc1=O`
ZINC4556825	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](O)[C@H](CO)O[C@@H]1n1ccc(N)nc1=O`
ZINC5998209	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC5998324	0.756	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@H](O)[C@@H](CO)O[C@H]1n1ccc(N)nc1=O`
ZINC2288831	0.750	296.3 Da LogP -0.28 TPSA 181.4	✓ Ro5	✓ Clean	`Nc1nc(N)nc(-c2ccc(-c3nc(N)nc(N)n3)cc2)n1`
ZINC5541164	0.750	435.4 Da LogP -5.38 TPSA 230.2	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O[C@H]3O[C@@H](C…`
ZINC5541165	0.750	435.4 Da LogP -5.38 TPSA 230.2	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O[C@H]3O[C@@H](…`
ZINC1572132	0.745	267.2 Da LogP -1.66 TPSA 139.3	✓ Ro5	✓ Clean	`Nc1nc(=O)[nH]c2c1ncn2[C@H]1C[C@H](O)[C@@H](CO)O1`
ZINC106384020	0.733	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](CO)O[C@@H](n2ccc(N)nc2=O)[C@@H]1O`
ZINC106384023	0.733	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](O)[C@H](n2ccc(N)nc2=O)O[C@@H]1CO`
ZINC256828171	0.733	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](CO)O[C@H](n2ccc(N)nc2=O)[C@H]1O`
ZINC256828175	0.733	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](CO)O[C@@H](n2ccc(N)nc2=O)[C@@H]1O`
ZINC256828178	0.733	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](CO)O[C@@H](n2ccc(N)nc2=O)[C@H]1O`
ZINC5998228	0.733	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@H]1[C@H](O)[C@H](n2ccc(N)nc2=O)O[C@@H]1CO`
ZINC95094424	0.733	257.2 Da LogP -1.91 TPSA 119.8	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](CO)O[C@H](n2ccc(N)nc2=O)[C@@H]1O`

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.