Protein profile

PA0584

multifunctional tRNA nucleotidyl transferase/2'3'-cyclic phosphodiesterase/2'nucleotidase/phosphatase

Genome: NC_002516.2

Gene: PA0584 cca Structure source: AlphaFold UniProt Q9I5V3

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Amino acids 410

Annotations 13

Features 26

PDB binders 4

Druggability 0.314

Overview

Basic information about this protein and its source genome.

Accession: PA0584
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA0584 cca
Status: annotated
Amino acids: 410
Structure source: AlphaFold

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0004810 Catalysis of the reaction: a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate. GO:0160016 Catalysis of the reaction: a tRNA with a 3' CCA end + 2 CTP + ATP = a tRNA with a 3' CCACCA end + 3 diphosphate. GO:0004112 Catalysis of the reaction: a nucleoside cyclic phosphate + H2O = a nucleoside phosphate. GO:0000287 Binding to a magnesium (Mg) ion. GO:0016791 Catalysis of the hydrolysis of a phosphoric monoester, releasing a phosphate.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 33.333
Human E-value: 1.77e-08
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 0.314

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

13 GO

Gene Ontology (GO)

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0004810 Catalysis of the reaction: a tRNA precursor + ATP + 2 CTP = a tRNA with a 3' CCA end + 3 diphosphate.
GO:0160016 Catalysis of the reaction: a tRNA with a 3' CCA end + 2 CTP + ATP = a tRNA with a 3' CCACCA end + 3 diphosphate.
GO:0004112 Catalysis of the reaction: a nucleoside cyclic phosphate + H2O = a nucleoside phosphate.
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0016791 Catalysis of the hydrolysis of a phosphoric monoester, releasing a phosphate.
GO:0000049 Binding to a transfer RNA.
GO:0042245 Any process that results in the repair of damaged RNA.
GO:0001680 Post-transcriptional addition of the terminal 3' CCA sequence to a tRNA which does not encode this sequence within the primary transcript. CCA addition proceeds by the sequential addition of CTP, CTP, and then ATP to the 3' end of the tRNA, yielding a diphosphate with each nucleotide addition.
GO:0106354 The set of processes involved in identifying and degrading defective or aberrant tRNAs.
GO:0016779 Catalysis of the transfer of a nucleotidyl group from one compound (donor) to another (acceptor).
GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
GO:0003723 Binding to an RNA molecule or a portion thereof.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records

Show feature table

Start	End	DB	Term	Name
1	403	PANTHER	PTHR47545	MULTIFUNCTIONAL CCA PROTEIN
120	401	SUPERFAMILY	SSF81891	Poly A polymerase C-terminal region-like
1	408	PIRSF	PIRSF000813	CCA_bact
1	408	InterPro	IPR012006	tRNA nucleotidyltransferase, proteobacteria
227	316	CDD	cd00077	HDc
227	316	InterPro	IPR003607	HD/PDEase domain
1	407	Hamap	MF_01261	Multifunctional CCA protein [cca].
1	407	InterPro	IPR012006	tRNA nucleotidyltransferase, proteobacteria
1	124	Gene3D	G3DSA:3.30.460.10	Beta Polymerase, domain 2
1	124	InterPro	IPR043519	Nucleotidyltransferase superfamily
149	212	Pfam	PF12627	Probable RNA and SrmB- binding site of polymerase A
149	212	InterPro	IPR032828	tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain
125	354	FunFam	G3DSA:1.10.3090.10:FF:000001	Multifunctional CCA protein
231	320	Pfam	PF01966	HD domain
231	320	InterPro	IPR006674	HD domain
4	122	Pfam	PF01743	Poly A polymerase head domain
4	122	InterPro	IPR002646	Poly A polymerase, head domain
125	352	Gene3D	G3DSA:1.10.3090.10	-
1	401	Hamap	MF_01262	CCA-adding enzyme [cca].
1	401	InterPro	IPR012006	tRNA nucleotidyltransferase, proteobacteria
1	118	CDD	cd05398	NT_ClassII-CCAase
1	118	InterPro	IPR002646	Poly A polymerase, head domain
228	329	ProSiteProfiles	PS51831	HD domain profile.
228	329	InterPro	IPR006674	HD domain
1	119	SUPERFAMILY	SSF81301	Nucleotidyltransferase
1	119	InterPro	IPR043519	Nucleotidyltransferase superfamily

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 PA0584	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
2				0.314

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.

54 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
2TM	6Q52	A0A1C7DQ98	481.2 Da LogP -2.10 TPSA 261.2	2 viol.	✓ Clean	`C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`
APC	1VFG	O66728	505.2 Da LogP -1.52 TPSA 269.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
FLC	4X4W	Q96Q11	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
POP	3WFR	O67911	176.0 Da LogP -2.08 TPSA 129.9	✓ Ro5	✓ Clean	`O[P@@](=O)([O-])O[P@@](=O)(O)[O-]`

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
ZINC104864216	0.808	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@](=O)(O)OP(=O)(O)O)[C…`
ZINC12504412	0.808	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC12504413	0.808	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC12504414	0.808	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC13431045	0.808	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC13431047	0.808	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC13548733	0.808	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC33913782	0.808	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC36471998	0.808	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(OP(=O)(O)O)OP(=O)(…`
ZINC8215624	0.808	403.2 Da LogP -2.33 TPSA 223.9	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)[…`
ZINC1532524	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC16546001	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC1785780	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@@H…`
ZINC1785781	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@@H]…`
ZINC3861744	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]…`
ZINC3869480	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H]…`
ZINC3869481	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC3869482	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@H…`
ZINC3869483	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC3954230	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC8613159	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC8952080	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC9007749	0.800	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC12502055	0.778	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC12502057	0.778	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC12502058	0.778	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC13431057	0.778	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC13431059	0.778	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC25726736	0.778	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC3861746	0.778	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@@](=O)(O)…`
ZINC53683723	0.778	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC82142138	0.778	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC82142140	0.778	483.2 Da LogP -2.21 TPSA 270.4	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC13540477	0.633	499.2 Da LogP -0.84 TPSA 253.3	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC218579342	0.633	499.2 Da LogP -0.84 TPSA 253.3	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC218579414	0.633	499.2 Da LogP -0.84 TPSA 253.3	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC218579482	0.633	499.2 Da LogP -0.84 TPSA 253.3	2 viol.	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(O…`
ZINC5139067	0.618	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CS)[C@@H](O)[C@H]1O`
ZINC1078621	0.615	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	0.615	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	0.615	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	0.615	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	0.615	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	0.615	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	0.615	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	0.615	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)…`
ZINC6091575	0.615	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	0.615	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	0.615	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	0.615	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`

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.