Protein profile

KP13_01462

Protein methyltransferase hemK

Genome: KpKP13

Gene: AHE44004.1 hemK Structure source: AlphaFold + ColabFold UniProt A0A0H3GPQ1

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Amino acids 283

Annotations 7

Features 26

PDB binders 6

Druggability 0.929

Overview

Basic information about this protein and its source genome.

Accession: KP13_01462
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44004.1 hemK
Status: annotated
Amino acids: 283
Structure source: AlphaFold + ColabFold

2.1.1.297

GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0003676 Binding to a nucleic acid. GO:0006479 The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom. GO:0032259 The process in which a methyl group is covalently attached to a molecule. GO:0008276 Catalysis of the transfer of a methyl group (CH3-) to a protein. GO:0102559 Catalysis of the reaction: L-glutaminyl-[peptide chain release factor] + S-adenosyl-L-methionine = N(5)-methyl-L-glutaminyl-[peptide chain release factor] + S-adenosyl-L-homocysteine + H+.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 29.889
Human E-value: 2.53e-17
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 75.182
DEG E-value: 8.8e-151
Localization: Cytoplasmic
ColabFold pLDDT: 94.71

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 0.929

Structure A0A0H3GPQ1

Pocket Pocket 1

P2Rank 0.733

Structure A0A0H3GPQ1

Pocket Pocket 1

ColabFold model

FPocket 0.67 · Pocket 1

P2Rank 0.754 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 157 / 4744 genomes with a hit

Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

2.1.1.297

Gene Ontology (GO)

GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0003676 Binding to a nucleic acid.
GO:0006479 The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.
GO:0008276 Catalysis of the transfer of a methyl group (CH3-) to a protein.
GO:0102559 Catalysis of the reaction: L-glutaminyl-[peptide chain release factor] + S-adenosyl-L-methionine = N(5)-methyl-L-glutaminyl-[peptide chain release factor] + S-adenosyl-L-homocysteine + H+.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records

Show feature table

Start	End	DB	Term	Name
8	275	PANTHER	PTHR18895	HEMK METHYLTRANSFERASE
111	247	Pfam	PF13847	Methyltransferase domain
111	247	InterPro	IPR025714	Methyltransferase domain
1	2	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
24	272	NCBIfam	TIGR03534	peptide chain release factor N(5)-glutamine methyltransferase
24	272	InterPro	IPR019874	Protein-(glutamine-N5) methyltransferase, release factor-specific
181	187	ProSitePatterns	PS00092	N-6 Adenine-specific DNA methylases signature.
181	187	InterPro	IPR002052	DNA methylase, N-6 adenine-specific, conserved site
19	283	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	18	Phobius	SIGNAL_PEPTIDE	Signal peptide region
2	84	Gene3D	G3DSA:1.10.8.10	-
2	84	FunFam	G3DSA:1.10.8.10:FF:000032	Release factor glutamine methyltransferase
113	238	CDD	cd02440	AdoMet_MTases
4	276	Hamap	MF_02126	Release factor glutamine methyltransferase [prmC].
4	276	InterPro	IPR019874	Protein-(glutamine-N5) methyltransferase, release factor-specific
14	18	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
86	277	FunFam	G3DSA:3.40.50.150:FF:000053	Release factor glutamine methyltransferase
86	276	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
86	276	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
7	74	Pfam	PF17827	PrmC N-terminal domain
7	74	InterPro	IPR040758	Release factor glutamine methyltransferase, N-terminal domain
2	276	NCBIfam	TIGR00536	HemK family protein methyltransferase
2	276	InterPro	IPR004556	Methyltransferase HemK-like
5	274	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
5	274	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
3	13	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.

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_A0A0H3GPQ1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01462	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				0.929

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	9.5	0.511
2	8.7	0.465
3	0.88	0.004

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				0.67

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	7.77	0.412
2	5.62	0.27
3	1.64	0.027

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.

56 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
7QM	5U1I	Q2MG72	497.5 Da LogP -7.06 TPSA 274.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H]([C@H](O[C@@H]([C@@H]1O)O[C@H]2[C…`
7XP	5U0N	Q2MG72	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C…`
827	5U19	Q2MG72	482.5 Da LogP -6.00 TPSA 248.4	2 viol.	✓ Clean	`C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H…`
9CS	5U1E	Q2MG72	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C…`
GET	5U18	Q2MG72	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`C[C@H]([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@…`
MEQ	1NV8	Q9WYV8	160.2 Da LogP -1.08 TPSA 92.4	✓ Ro5	✓ Clean	`CNC(=O)CC[C@@H](C(=O)O)N`

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
ZINC100069123	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](O)[C@H](O[…`
ZINC106588639	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@@H](…`
ZINC1772820029	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H]…`
ZINC1857790211	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@…`
ZINC1857790212	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@…`
ZINC252460108	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@@H](…`
ZINC253380792	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@@H]2[C@H](N)C[C@H](N…`
ZINC253380793	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@@H]2[C@H](N)C[C@H](N…`
ZINC253380794	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@H]2[C@@H](O)[C@@H](O…`
ZINC253380795	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@H]2[C@@H](O)[C@@H](O…`
ZINC256001609	1.000	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC256001610	1.000	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC256001611	1.000	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC256001612	1.000	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC43543817	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H]…`
ZINC49708768	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H]…`
ZINC53132258	1.000	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC60183639	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC60183641	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC60183644	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC60183647	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC60184326	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](O)[C@H](O[…`
ZINC64857811	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H](…`
ZINC70691602	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@H]…`
ZINC70691603	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@H]…`
ZINC70691604	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@@H](…`
ZINC70691605	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@@H](…`
ZINC72332859	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@H]…`
ZINC72332860	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@H]…`
ZINC77301567	1.000	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@H]2[C@H](N)C[C@H](N)[C@@H](O…`
ZINC936069019	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@H](N)C[C@H](…`
ZINC936069020	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@H](N)C[C@H](…`
ZINC936069021	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@H](N)C[C@H](…`
ZINC936069022	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@H](N)C[C@H](…`
ZINC17654095	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@…`
ZINC239203291	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC239203292	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC242649358	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649360	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649362	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC245224172	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224173	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224174	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224175	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC43470138	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H…`
ZINC8101132	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@H]3O…`
ZINC8101133	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@H]3O…`
ZINC8101134	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@H](O[C@H]3O[…`
ZINC8101135	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@H](O[C@H]3O[…`
ZINC8214590	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`

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.