Protein profile

VK055_3907

polyribonucleotide nucleotidyltransferase

Genome: KpATCC43816

Gene: AIK82455.1 pnp Structure source: AlphaFold + ColabFold UniProt A0A0H3GY04

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Amino acids 690

Annotations 9

Features 60

PDB binders 5

Druggability 0.435

Overview

Basic information about this protein and its source genome.

Accession: VK055_3907
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK82455.1 pnp
Status: annotated
Amino acids: 690
Structure source: AlphaFold + ColabFold

2.7.7.8

GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. GO:0003676 Binding to a nucleic acid. GO:0006402 The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes. GO:0004654 Catalysis of the reaction: RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 44.578
Human E-value: 2.23e-08
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 95.942
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 92.72

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 0.435

Structure A0A0H3GY04

Pocket Pocket 11

P2Rank 0.878

Structure A0A0H3GY04

Pocket Pocket 1

ColabFold model

FPocket 0.382 · Pocket 24

P2Rank 0.826 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 577 / 4744 genomes with a hit

Normalized 0.122

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)

2.7.7.8

Gene Ontology (GO)

GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
GO:0003676 Binding to a nucleic acid.
GO:0006402 The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
GO:0004654 Catalysis of the reaction: RNA(n+1) + phosphate = RNA(n) + a nucleoside diphosphate.
GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
GO:0000287 Binding to a magnesium (Mg) ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

60 records

Show feature table

Start	End	DB	Term	Name
533	601	SUPERFAMILY	SSF54791	Eukaryotic type KH-domain (KH-domain type I)
533	601	InterPro	IPR036612	K Homology domain, type 1 superfamily
429	527	SUPERFAMILY	SSF55666	Ribonuclease PH domain 2-like
429	527	InterPro	IPR036345	Exoribonuclease, PH domain 2 superfamily
280	471	SUPERFAMILY	SSF54211	Ribosomal protein S5 domain 2-like
280	471	InterPro	IPR020568	Ribosomal protein S5 domain 2-type fold
600	670	Gene3D	G3DSA:2.40.50.140	-
600	670	InterPro	IPR012340	Nucleic acid-binding, OB-fold
531	596	SMART	SM00322	kh_6
531	596	InterPro	IPR004087	K Homology domain
601	669	ProSiteProfiles	PS50126	S1 domain profile.
601	669	InterPro	IPR003029	S1 domain
303	523	CDD	cd11364	RNase_PH_PNPase_2
2	212	CDD	cd11363	RNase_PH_PNPase_1
126	189	Pfam	PF03725	3' exoribonuclease family, domain 2
126	189	InterPro	IPR015847	Exoribonuclease, phosphorolytic domain 2
439	506	Pfam	PF03725	3' exoribonuclease family, domain 2
439	506	InterPro	IPR015847	Exoribonuclease, phosphorolytic domain 2
532	591	ProSiteProfiles	PS50084	Type-1 KH domain profile.
2	677	PANTHER	PTHR11252	POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE
2	677	InterPro	IPR012162	Polyribonucleotide nucleotidyltransferase
598	669	Pfam	PF00575	S1 RNA binding domain
598	669	InterPro	IPR003029	S1 domain
2	123	SUPERFAMILY	SSF54211	Ribosomal protein S5 domain 2-like
2	123	InterPro	IPR020568	Ribosomal protein S5 domain 2-type fold
601	668	CDD	cd04472	S1_PNPase
668	690	MobiDBLite	mobidb-lite	consensus disorder prediction
1	672	Hamap	MF_01595	Polyribonucleotide nucleotidyltransferase [pnp].
1	672	InterPro	IPR012162	Polyribonucleotide nucleotidyltransferase
529	599	Gene3D	G3DSA:3.30.1370.10	K Homology domain, type 1
529	599	InterPro	IPR036612	K Homology domain, type 1 superfamily
221	299	Pfam	PF03726	Polyribonucleotide nucleotidyltransferase, RNA binding domain
221	299	InterPro	IPR015848	Polyribonucleotide nucleotidyltransferase, RNA-binding domain
3	123	Pfam	PF01138	3' exoribonuclease family, domain 1
3	123	InterPro	IPR001247	Exoribonuclease, phosphorolytic domain 1
303	435	Pfam	PF01138	3' exoribonuclease family, domain 1
303	435	InterPro	IPR001247	Exoribonuclease, phosphorolytic domain 1
1	213	Gene3D	G3DSA:3.30.230.70	-
1	213	InterPro	IPR027408	PNPase/RNase PH domain superfamily
214	528	Gene3D	G3DSA:3.30.230.70	-
214	528	InterPro	IPR027408	PNPase/RNase PH domain superfamily
535	593	Pfam	PF00013	KH domain
535	593	InterPro	IPR004088	K Homology domain, type 1
2	670	NCBIfam	TIGR03591	polyribonucleotide nucleotidyltransferase
2	670	InterPro	IPR012162	Polyribonucleotide nucleotidyltransferase
1	689	PIRSF	PIRSF005499	PNPase
1	689	InterPro	IPR012162	Polyribonucleotide nucleotidyltransferase
530	599	CDD	cd02393	KH-I_PNPase
124	214	SUPERFAMILY	SSF55666	Ribonuclease PH domain 2-like
124	214	InterPro	IPR036345	Exoribonuclease, PH domain 2 superfamily
601	671	FunFam	G3DSA:2.40.50.140:FF:000023	Polyribonucleotide nucleotidyltransferase
529	597	FunFam	G3DSA:3.30.1370.10:FF:000001	Polyribonucleotide nucleotidyltransferase
205	304	SUPERFAMILY	SSF46915	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
205	304	InterPro	IPR036456	Polyribonucleotide nucleotidyltransferase, RNA-binding domain superfamily
599	669	SMART	SM00316	S1_6
599	669	InterPro	IPR022967	RNA-binding domain, S1
214	528	FunFam	G3DSA:3.30.230.70:FF:000002	Polyribonucleotide nucleotidyltransferase
1	213	FunFam	G3DSA:3.30.230.70:FF:000001	Polyribonucleotide nucleotidyltransferase
587	671	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
587	671	InterPro	IPR012340	Nucleic acid-binding, OB-fold

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_A0A0H3GY04	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3907	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
41				0.133
43				0.091
2				0.005
42				0.002

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	27.06	0.878
2	12.83	0.582
3	3.59	0.107
4	2.52	0.057
5	2.5	0.056

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				0.013
33				0.002
39				0.0
50				0.0

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	22.38	0.826
2	10.96	0.506
3	4.22	0.142
4	2.8	0.07
5	2.38	0.051

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.

55 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
5GP	3GCM	A7ZS61	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…`
FLC	3GCM	A7ZS61	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
PPV	5XEX	Q2FZ20	178.0 Da LogP -0.81 TPSA 124.3	✓ Ro5	✓ Clean	`OP(=O)(O)OP(=O)(O)O`
VGL	4NNI	P9WH43	124.1 Da LogP 0.17 TPSA 63.1	✓ Ro5	✓ Clean	`c1cnc(cn1)C(=O)O`
WO4	3H1C	P05055	247.8 Da LogP -2.62 TPSA 80.3	✓ Ro5	✓ Clean	`[O-][W](=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
ZINC12501413	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC12958448	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC1532555	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC16546189	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC2159505	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3073318	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869963	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869965	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC9334496	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC104869865	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…`
ZINC12504289	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC34541308	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC35000839	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC45284491	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC80639694	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC8215481	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC33979258	0.800	364.2 Da LogP -2.45 TPSA 200.2	1 viol.	✓ Clean	`O=c1[nH]c(O)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)…`
ZINC33979259	0.800	364.2 Da LogP -2.45 TPSA 200.2	1 viol.	✓ Clean	`O=c1[nH]c(O)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)…`
ZINC78920152	0.800	364.2 Da LogP -2.45 TPSA 200.2	1 viol.	✓ Clean	`O=c1[nH]c(O)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)…`
ZINC71774763	0.758	432.3 Da LogP -2.23 TPSA 198.3	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@](=O)(O)N3CCOCC3…`
ZINC12296728	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)…`
ZINC13527599	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O…`
ZINC13527603	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)…`
ZINC1532627	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)…`
ZINC1730395	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O…`
ZINC3869846	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O…`
ZINC3869847	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2…`
ZINC3869848	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O…`
ZINC4743771	0.741	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC4743772	0.741	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC4743774	0.741	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC4743775	0.741	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC14951284	0.732	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C…`
ZINC1532551	0.732	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@…`
ZINC16969369	0.732	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@…`
ZINC4228242	0.732	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@…`
ZINC4353761	0.732	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C…`
ZINC8614392	0.732	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C…`
ZINC12503440	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC1530370	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](OP(=O)(O)O)[…`
ZINC28631009	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](OP(=O)(O)O)[…`
ZINC3872740	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC3872741	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…`
ZINC3872742	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC3872743	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…`
ZINC1570863	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(…`
ZINC38580950	0.722	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc32)[C@H](O…`
ZINC3869969	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)…`
ZINC4990802	0.722	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc32)[C@@H]…`
ZINC8613125	0.722	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c…`

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.