Protein profile

KP13_01854

Poly(A) polymerase

Genome: KpKP13

Gene: AHE46294.1 pcnB Structure source: AlphaFold + ColabFold UniProt A0A0H3GJH7

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Amino acids 453

Annotations 9

Features 23

PDB binders 4

Druggability 0.511

Overview

Basic information about this protein and its source genome.

Accession: KP13_01854
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46294.1 pcnB
Status: annotated
Amino acids: 453
Structure source: AlphaFold + ColabFold

2.7.7.19

GO:0006378 OBSOLETE. The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript. GO:1990817 Catalysis of the reaction: ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide. The primer may be an RNA or DNA fragment, or oligo(A) bearing a 3'-OH terminal group. 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. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 43.137
Human E-value: 6.25e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 40.194
DEG E-value: 3.18e-97
Localization: Cytoplasmic
ColabFold pLDDT: 84.49

Selected Druggability evidence

AlphaFold / UniProt model

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 0.511

Structure A0A0H3GJH7

Pocket Pocket 2

P2Rank 0.644

Structure A0A0H3GJH7

Pocket Pocket 1

ColabFold model

FPocket 0.374 · Pocket 35

P2Rank 0.599 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 151 / 4744 genomes with a hit

Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

2.7.7.19

Gene Ontology (GO)

GO:0006378 OBSOLETE. The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
GO:1990817 Catalysis of the reaction: ATP + RNA(n) = diphosphate + RNA(n)-3'-adenine ribonucleotide. The primer may be an RNA or DNA fragment, or oligo(A) bearing a 3'-OH terminal group.
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.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0006397 Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
GO:0043633 The chemical reactions and pathways resulting in the breakdown of an RNA molecule, initiated by the enzymatic addition of a sequence of adenylyl residues (polyadenylation) at the 3'-end of the target RNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
14	449	Hamap	MF_00957	Poly(A) polymerase I [pcnB].
14	449	InterPro	IPR010206	Poly(A) polymerase I
327	446	Pfam	PF12626	Polymerase A arginine-rich C-terminus
327	446	InterPro	IPR025866	Polymerase A arginine-rich C-terminal domain
52	182	Pfam	PF01743	Poly A polymerase head domain
52	182	InterPro	IPR002646	Poly A polymerase, head domain
34	178	CDD	cd05398	NT_ClassII-CCAase
34	178	InterPro	IPR002646	Poly A polymerase, head domain
180	431	Gene3D	G3DSA:1.10.3090.10	-
10	332	PANTHER	PTHR43051	POLYNUCLEOTIDE ADENYLYLTRANSFERASE FAMILY PROTEIN
438	453	MobiDBLite	mobidb-lite	consensus disorder prediction
18	179	Gene3D	G3DSA:3.30.460.10	Beta Polymerase, domain 2
18	179	InterPro	IPR043519	Nucleotidyltransferase superfamily
209	270	Pfam	PF12627	Probable RNA and SrmB- binding site of polymerase A
209	270	InterPro	IPR032828	tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain
17	178	FunFam	G3DSA:3.30.460.10:FF:000035	Poly(A) polymerase I
180	417	SUPERFAMILY	SSF81891	Poly A polymerase C-terminal region-like
180	431	FunFam	G3DSA:1.10.3090.10:FF:000003	Poly(A) polymerase I
20	447	NCBIfam	TIGR01942	polynucleotide adenylyltransferase PcnB
20	447	InterPro	IPR010206	Poly(A) polymerase I
23	178	SUPERFAMILY	SSF81301	Nucleotidyltransferase
23	178	InterPro	IPR043519	Nucleotidyltransferase superfamily
422	453	MobiDBLite	mobidb-lite	consensus disorder prediction

3D Structure

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

Loading 3D structure...

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Structural evidence

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GJH7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01854	ColabFold	—	—	full sequence	—	Loaded

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				0.511

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	8.11	0.432
2	2.17	0.051
3	1.25	0.012

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
35				0.374
32				0.298

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	8.41	0.449
2	3.82	0.148
3	1.86	0.036

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.