Protein profile

KP13_01394

Protein pemK

Genome: KpKP13

Gene: AHE47436.1 pemK Structure source: AlphaFold + ColabFold UniProt R9R7H5

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Amino acids 110

Annotations 6

Features 9

PDB binders 2

Druggability 0.053

Overview

Basic information about this protein and its source genome.

Accession: KP13_01394
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE47436.1 pemK
Status: annotated
Amino acids: 110
Structure source: AlphaFold + ColabFold

3.1.-.-

GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0004521 Catalysis of the cleavage of ester linkages within ribonucleic acid by creating internal breaks. 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:0016075 The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Unknown
ColabFold pLDDT: 93.24

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 0.053

Structure R9R7H5

Pocket Pocket 4

P2Rank 0.007

Structure R9R7H5

Pocket Pocket 1

ColabFold model

FPocket 0.429 · Pocket 1

P2Rank 0.001 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 26 / 4744 genomes with a hit

Normalized 0.005

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

3.1.-.-

Gene Ontology (GO)

GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0004521 Catalysis of the cleavage of ester linkages within ribonucleic acid by creating internal breaks.
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:0016075 The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.

Sequence Features

Domain/signature hits from InterPro and related databases.

9 records

Show feature table

Start	End	DB	Term	Name
1	109	SUPERFAMILY	SSF50118	Cell growth inhibitor/plasmid maintenance toxic component
1	110	Gene3D	G3DSA:2.30.30.110	-
1	110	InterPro	IPR011067	Plasmid maintenance toxin/Cell growth inhibitor
1	110	PIRSF	PIRSF033490	MazF
1	110	InterPro	IPR003477	mRNA interferase PemK-like
1	109	PANTHER	PTHR33988	ENDORIBONUCLEASE MAZF-RELATED
1	109	InterPro	IPR003477	mRNA interferase PemK-like
2	108	Pfam	PF02452	PemK-like, MazF-like toxin of type II toxin-antitoxin system
2	108	InterPro	IPR003477	mRNA interferase PemK-like

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_R9R7H5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01394	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
1				0.429
2				0.299

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.

53 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
1PG	1NE8	P96622	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
3PO	7D2M	Q9RX98	258.0 Da LogP -0.69 TPSA 170.8	✓ Ro5	✓ Clean	`OP(=O)(O)OP(=O)(O)OP(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL1324227	P0AE70	6.57	395.4 Da LogP 1.81 TPSA 115.5	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3C(C(=O)c4ccc5ccccc5n4)=N…`

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
ZINC103543913	1.000	395.4 Da LogP 1.81 TPSA 115.5	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3C(C(=O)c4ccc5ccccc5n4)=N…`
ZINC103543928	1.000	395.4 Da LogP 1.81 TPSA 115.5	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@H]3NN=C(C(=O)c4ccc5ccccc5n4)…`
ZINC1580161	1.000	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16037518	1.000	395.4 Da LogP 1.81 TPSA 115.5	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3NN=C(C(=O)c4ccc5ccccc5n4…`
ZINC16052118	1.000	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	1.000	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC18202958	1.000	395.4 Da LogP 1.81 TPSA 115.5	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@H]3NN=C(C(=O)c4ccc5ccccc5n4)…`
ZINC34317654	1.000	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	1.000	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	1.000	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	1.000	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6827739	1.000	258.0 Da LogP -0.69 TPSA 170.8	✓ Ro5	✓ Clean	`O=P(O)(O)OP(=O)(O)OP(=O)(O)O`
ZINC575419714	0.727	312.4 Da LogP 0.42 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCSCCOCCOCCO`
ZINC115163232	0.700	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCCO`
ZINC258837490	0.700	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCCO`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1692489	0.688	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC3874716	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC4530388	0.688	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5178829	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5701172	0.688	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC5997861	0.688	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC6476653	0.677	388.4 Da LogP 2.07 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(C1=NN[C@@H]2C(=O)N(c3cccc(F)c3)C(=O)[C@H]12…`
ZINC575432150	0.667	344.4 Da LogP -0.89 TPSA 100.5	✓ Ro5	✓ Clean	`COCCOCCOCCS(=O)(=O)CCOCCOCCO`
ZINC16034323	0.656	438.4 Da LogP 2.95 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(C1=NN[C@@H]2C(=O)N(c3cccc(C(F)(F)F)c3)C(=O)…`
ZINC17920729	0.656	400.4 Da LogP 1.94 TPSA 101.0	✓ Ro5	✓ Clean	`COc1cccc(N2C(=O)[C@H]3NN=C(C(=O)c4ccc5ccccc5n4)…`
ZINC100671216	0.656	346.3 Da LogP 0.05 TPSA 128.4	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@H]3NN=C(C(=O)c4cnccn4)[C@H]3…`
ZINC101363284	0.656	346.3 Da LogP 0.05 TPSA 128.4	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@H]3NN=C(C(=O)c4cnccn4)[C@@H]…`
ZINC16037367	0.656	346.3 Da LogP 0.05 TPSA 128.4	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3C(C(=O)c4cnccn4)=NN[C@H]…`
ZINC18124993	0.656	346.3 Da LogP 0.05 TPSA 128.4	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3NN=C(C(=O)c4cnccn4)[C@@H…`
ZINC1857524240	0.652	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`COCCNCCOCCOCCO`
ZINC107287805	0.635	438.4 Da LogP 2.95 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(C1=NN[C@H]2C(=O)N(c3ccccc3C(F)(F)F)C(=O)[C@…`
ZINC107287807	0.635	438.4 Da LogP 2.95 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(C1=NN[C@@H]2C(=O)N(c3ccccc3C(F)(F)F)C(=O)[C…`
ZINC16034338	0.635	438.4 Da LogP 2.95 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(C1=NN[C@H]2C(=O)N(c3ccccc3C(F)(F)F)C(=O)[C@…`
ZINC18153132	0.635	438.4 Da LogP 2.95 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(C1=NN[C@@H]2C(=O)N(c3ccccc3C(F)(F)F)C(=O)[C…`
ZINC103462792	0.633	322.3 Da LogP 0.75 TPSA 91.7	✓ Ro5	✓ Clean	`CCN1C(=O)[C@H]2NN=C(C(=O)c3ccc4ccccc4n3)[C@@H]2…`
ZINC103462794	0.633	322.3 Da LogP 0.75 TPSA 91.7	✓ Ro5	✓ Clean	`CCN1C(=O)[C@H]2NN=C(C(=O)c3ccc4ccccc4n3)[C@H]2C…`
ZINC103462795	0.633	322.3 Da LogP 0.75 TPSA 91.7	✓ Ro5	✓ Clean	`CCN1C(=O)[C@@H]2NN=C(C(=O)c3ccc4ccccc4n3)[C@@H]…`
ZINC5455887	0.633	322.3 Da LogP 0.75 TPSA 91.7	✓ Ro5	✓ Clean	`CCN1C(=O)[C@@H]2C(C(=O)c3ccc4ccccc4n3)=NN[C@H]2…`
ZINC17835620	0.625	400.4 Da LogP 1.94 TPSA 101.0	✓ Ro5	✓ Clean	`COc1ccccc1N1C(=O)[C@H]2NN=C(C(=O)c3ccc4ccccc4n3…`
ZINC100673359	0.613	434.5 Da LogP 2.78 TPSA 102.6	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@H]3NN=C(C(=O)C(c4ccccc4)c4cc…`
ZINC103544561	0.613	434.5 Da LogP 2.78 TPSA 102.6	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3C(C(=O)C(c4ccccc4)c4cccc…`
ZINC103544567	0.613	434.5 Da LogP 2.78 TPSA 102.6	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@H]3NN=C(C(=O)C(c4ccccc4)c4cc…`
ZINC9411194	0.613	434.5 Da LogP 2.78 TPSA 102.6	✓ Ro5	✓ Clean	`N#Cc1ccc(N2C(=O)[C@@H]3NN=C(C(=O)C(c4ccccc4)c4c…`
ZINC257355138	0.600	479.9 Da LogP 0.65 TPSA 287.0	2 viol.	✓ Clean	`O=P(=O)O[P@](=O)(O)O[P@](=O)(O)O[P@@](=O)(O)O[P…`
ZINC5650743	0.600	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	0.600	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`

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.