Protein profile

VK055_1025

putative O-METHYLTRANSFERASE

Genome: KpATCC43816

Gene: AIK79648.1 Structure source: Experimental + ColabFold UniProt A6T8J6

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Amino acids 219

Annotations 1

Features 10

PDB binders 11

Druggability 0.44

Overview

Basic information about this protein and its source genome.

Accession: VK055_1025
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79648.1
Status: annotated
Amino acids: 219
Structure source: Experimental + ColabFold

GO:0008171 Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 36.538
Human E-value: 5.7e-11
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 98.47

Selected Druggability evidence

PDB experimental structure

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 0.44

Structure 3TFW

Pocket Pocket 2

P2Rank 0.256

Structure 3TFW

Pocket Pocket 1

ColabFold model

FPocket 0.824 · Pocket 1

P2Rank 0.421 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 56 / 4744 genomes with a hit

Normalized 0.012

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

GO:0008171 Catalysis of the transfer of a methyl group to the oxygen atom of an acceptor molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records

Show feature table

Start	End	DB	Term	Name
1	219	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
1	219	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
23	205	Pfam	PF01596	O-methyltransferase
23	205	InterPro	IPR002935	Class I-like SAM-dependent O-methyltransferase
1	218	ProSiteProfiles	PS51682	SAM-dependent O-methyltransferase class I-type profile.
1	218	InterPro	IPR002935	Class I-like SAM-dependent O-methyltransferase
59	160	CDD	cd02440	AdoMet_MTases
22	214	PANTHER	PTHR10509	O-METHYLTRANSFERASE-RELATED
3	215	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
3	215	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily

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

1 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 3TFW	X-ray	20.00 Å	-	—	PDBe RCSB PDBj File	Viewing
ColabFold VK055_1025	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
5				0.44
10				0.32

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	7.75	0.411
2	7.24	0.377
3	7.18	0.373
4	5.67	0.274
5	4.18	0.17

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				0.824

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	3.76	0.144
2	3.01	0.099
3	2.18	0.052
4	1.57	0.024

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.

63 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
2F6	4P58	O88587	162.2 Da LogP 1.12 TPSA 46.5	✓ Ro5	✓ Clean	`Cc1c(cn(n1)C)c2cc[nH]n2`
4FE	3CBG	Q55813	194.2 Da LogP 1.50 TPSA 66.8	✓ Ro5	✓ Clean	`COc1ccc(cc1O)\C=C\C(=O)O`
BU3	5LHM	Q50859	90.1 Da LogP -0.25 TPSA 40.5	✓ Ro5	✓ Clean	`C[C@H]([C@@H](C)O)O`
EAO	6LFE	P22734-2	265.2 Da LogP 1.57 TPSA 117.7	✓ Ro5	Alert	`CC(=O)C(=Cc1cc(c(c(c1)O)O)[N+](=O)[O-])C(=O)C`
FBN	3A7D	P22734-2	528.4 Da LogP -1.43 TPSA 262.7	3 viol.	Alert	`c1c(cc(c(c1C(=O)NCc2cn(nn2)C[C@@H]3[C@H]([C@H](…`
FER	3CBG	Q55813	194.2 Da LogP 1.50 TPSA 66.8	✓ Ro5	✓ Clean	`COc1cc(ccc1O)\C=C\C(=O)O`
FGQ	6GY1	P22734-2	317.3 Da LogP 3.22 TPSA 67.3	✓ Ro5	✓ Clean	`Cc1ccc(cc1)S(=O)(=O)c2cc(c(c3c2cccn3)O)F`
FRE	1SUI	Q40313	959.7 Da LogP -0.20 TPSA 413.3	3 viol.	Alert	`CC(C)(CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]…`
KOM	2ZVJ	P22734-2	254.2 Da LogP 2.87 TPSA 70.7	✓ Ro5	Alert	`c1ccc(cc1)C2=CC(=O)Oc3c2ccc(c3O)O`
LDP	5LOG	Q50859	153.2 Da LogP 0.60 TPSA 66.5	✓ Ro5	Alert	`c1cc(c(cc1CCN)O)O`
SPF	1SUS	Q40313	971.7 Da LogP -0.15 TPSA 402.3	3 viol.	✓ Clean	`CC1([C@H](C1(C(=O)NCCC(=O)NCCSC(=O)\C=C\c2cc(c(…`

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
CHEMBL1089318	O88587	8.82	413.2 Da LogP 3.28 TPSA 149.5	✓ Ro5	Alert	`Cc1c(Cl)c(C)[n+]([O-])c(Cl)c1-c1noc(-c2cc(O)c(O…`
CHEMBL166486	O88587	—	231.2 Da LogP 1.44 TPSA 131.2	✓ Ro5	Alert	`N#CC(C#N)=Cc1cc(O)c(O)c([N+](=O)[O-])c1`

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
ZINC1857643833	1.000	317.3 Da LogP 3.22 TPSA 67.3	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)c2cc(F)c(O)c3ncccc23)cc1`
ZINC34602275	1.000	413.2 Da LogP 3.28 TPSA 149.5	✓ Ro5	Alert	`Cc1c(Cl)c(C)[n+]([O-])c(Cl)c1-c1noc(-c2cc(O)c(O…`
ZINC406883	1.000	254.2 Da LogP 2.87 TPSA 70.7	✓ Ro5	Alert	`O=c1cc(-c2ccccc2)c2ccc(O)c(O)c2o1`
ZINC504786956	0.793	427.2 Da LogP 3.58 TPSA 138.5	✓ Ro5	✓ Clean	`COc1cc(-c2nc(-c3c(C)c(Cl)c(C)[n+]([O-])c3Cl)no2…`
ZINC13511212	0.769	342.3 Da LogP 3.38 TPSA 96.2	✓ Ro5	✓ Clean	`COc1cc(/C=C/c2cc(/C=C/C(=O)O)cc(OC)c2O)ccc1O`
ZINC116202	0.758	208.2 Da LogP 1.80 TPSA 55.8	✓ Ro5	✓ Clean	`COc1ccc(/C=C/C(=O)O)cc1OC`
ZINC1857775664	0.758	208.2 Da LogP 1.80 TPSA 55.8	✓ Ro5	✓ Clean	`COc1ccc(C=CC(=O)O)cc1OC`
ZINC6007189	0.758	208.2 Da LogP 1.80 TPSA 55.8	✓ Ro5	✓ Clean	`COc1ccc(/C=C\C(=O)O)cc1OC`
ZINC12358996	0.743	208.2 Da LogP 1.59 TPSA 55.8	✓ Ro5	✓ Clean	`COC(=O)/C=C\c1ccc(O)c(OC)c1`
ZINC1621053	0.743	208.2 Da LogP 1.59 TPSA 55.8	✓ Ro5	✓ Clean	`COC(=O)/C=C/c1ccc(O)c(OC)c1`
ZINC17255287	0.743	368.4 Da LogP 3.37 TPSA 93.1	✓ Ro5	✓ Clean	`COc1cc(/C=C\C(=O)CC(=O)/C=C/c2ccc(O)c(OC)c2)ccc…`
ZINC1857743026	0.743	368.4 Da LogP 3.37 TPSA 93.1	✓ Ro5	✓ Clean	`COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(OC)c2)ccc1O`
ZINC1903846672	0.743	208.2 Da LogP 1.59 TPSA 55.8	✓ Ro5	✓ Clean	`COC(=O)C=Cc1ccc(O)c(OC)c1`
ZINC2040753044	0.743	208.2 Da LogP 1.59 TPSA 55.8	✓ Ro5	✓ Clean	`COC(=O)C=Cc1ccc(OC)c(O)c1`
ZINC31261437	0.743	368.4 Da LogP 3.37 TPSA 93.1	✓ Ro5	✓ Clean	`COc1cc(/C=C\C(=O)CC(=O)/C=C\c2ccc(O)c(OC)c2)ccc…`
ZINC31430036	0.743	208.2 Da LogP 1.59 TPSA 55.8	✓ Ro5	✓ Clean	`COC(=O)/C=C\c1ccc(OC)c(O)c1`
ZINC6018515	0.743	208.2 Da LogP 1.59 TPSA 55.8	✓ Ro5	✓ Clean	`COC(=O)/C=C/c1ccc(OC)c(O)c1`
ZINC899824	0.743	368.4 Da LogP 3.37 TPSA 93.1	✓ Ro5	✓ Clean	`COc1cc(/C=C/C(=O)CC(=O)/C=C/c2ccc(O)c(OC)c2)ccc…`
ZINC42239	0.737	252.3 Da LogP 3.47 TPSA 50.4	✓ Ro5	✓ Clean	`Cc1c(O)ccc2c(-c3ccccc3)cc(=O)oc12`
ZINC100067274	0.730	368.4 Da LogP 3.85 TPSA 96.2	✓ Ro5	✓ Clean	`COc1cc(/C=C/C(=O)/C=C(O)/C=C/c2ccc(O)c(OC)c2)cc…`
ZINC104896565	0.730	368.4 Da LogP 3.85 TPSA 96.2	✓ Ro5	✓ Clean	`COc1cc(/C=C\C(=O)/C=C(O)/C=C/c2ccc(O)c(OC)c2)cc…`
ZINC828809065	0.718	268.3 Da LogP 2.66 TPSA 70.7	✓ Ro5	✓ Clean	`O=c1cc(-c2ccccc2)c2ccc(O)c(CO)c2o1`
ZINC67317204	0.711	315.4 Da LogP 2.79 TPSA 87.5	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)c2cc(O)c3cccnc3c2O)cc1`
ZINC3921797	0.711	254.3 Da LogP 3.30 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(/C=C/C(=O)c2ccccc2)cc1O`
ZINC3921800	0.711	254.3 Da LogP 3.30 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(/C=C/C(=O)c2ccccc2)ccc1O`
ZINC95648	0.711	288.3 Da LogP 4.32 TPSA 50.4	✓ Ro5	✓ Clean	`O=c1cc(-c2ccccc2)c2ccc3c(O)cccc3c2o1`
ZINC185070	0.710	272.3 Da LogP 3.29 TPSA 58.9	✓ Ro5	✓ Clean	`COc1cc(/C=C/c2ccc(O)c(OC)c2)ccc1O`
ZINC2040417310	0.703	208.2 Da LogP 1.89 TPSA 66.8	✓ Ro5	✓ Clean	`CCOc1cc(C=CC(=O)O)ccc1O`
ZINC2168918	0.703	208.2 Da LogP 1.89 TPSA 66.8	✓ Ro5	✓ Clean	`CCOc1cc(/C=C/C(=O)O)ccc1O`
ZINC33956762	0.703	234.3 Da LogP 3.03 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(/C=C/C(=O)C(C)(C)C)ccc1O`
ZINC114053603	0.702	397.2 Da LogP 4.04 TPSA 135.4	✓ Ro5	Alert	`Cc1nc(Cl)c(-c2noc(-c3cc(O)c(O)c([N+](=O)[O-])c3…`
ZINC120440	0.694	257.1 Da LogP 2.56 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(/C=C/C(=O)O)cc1Br`
ZINC1911787246	0.694	257.1 Da LogP 2.56 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(C=CC(=O)O)cc1Br`
ZINC2053515671	0.694	212.6 Da LogP 2.45 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(C=CC(=O)O)cc1Cl`
ZINC479915	0.694	212.6 Da LogP 2.45 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(/C=C/C(=O)O)cc1Cl`
ZINC5908418	0.694	212.6 Da LogP 2.45 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(/C=C\C(=O)O)cc1Cl`
ZINC6007078	0.694	257.1 Da LogP 2.56 TPSA 46.5	✓ Ro5	✓ Clean	`COc1ccc(/C=C\C(=O)O)cc1Br`
ZINC84193145	0.694	212.6 Da LogP 2.45 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(/C=C/C(=O)O)ccc1Cl`
ZINC88326938	0.694	257.1 Da LogP 2.56 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(/C=C/C(=O)O)ccc1Br`
ZINC2053571206	0.686	210.2 Da LogP 1.20 TPSA 87.0	✓ Ro5	Alert	`COc1cc(C=CC(=O)O)cc(O)c1O`
ZINC895821	0.686	210.2 Da LogP 1.20 TPSA 87.0	✓ Ro5	Alert	`COc1cc(/C=C/C(=O)O)cc(O)c1O`
ZINC2356428976	0.684	354.4 Da LogP 3.07 TPSA 104.1	✓ Ro5	Alert	`COc1cc(C=CC(=O)CC(=O)C=Cc2ccc(O)c(O)c2)ccc1O`
ZINC34581303	0.684	234.3 Da LogP 1.96 TPSA 63.6	✓ Ro5	✓ Clean	`COc1cc(/C=C/C(=O)CC(C)=O)ccc1O`
ZINC5543044	0.684	354.4 Da LogP 3.07 TPSA 104.1	✓ Ro5	Alert	`COc1cc(/C=C/C(=O)CC(=O)/C=C/c2ccc(O)c(O)c2)ccc1O`
ZINC386241	0.683	280.3 Da LogP 3.37 TPSA 67.5	✓ Ro5	✓ Clean	`CC(=O)c1c(O)ccc2c(-c3ccccc3)cc(=O)oc12`
ZINC486047	0.683	284.3 Da LogP 2.88 TPSA 79.9	✓ Ro5	Alert	`COc1ccc(-c2cc(=O)oc3c(O)c(O)ccc23)cc1`
ZINC153654	0.676	224.2 Da LogP 1.51 TPSA 76.0	✓ Ro5	✓ Clean	`COc1cc(/C=C/C(=O)O)cc(OC)c1O`
ZINC1903870248	0.676	224.2 Da LogP 1.51 TPSA 76.0	✓ Ro5	✓ Clean	`COc1cc(C=CC(=O)O)cc(OC)c1O`
ZINC6004394	0.676	224.2 Da LogP 1.51 TPSA 76.0	✓ Ro5	✓ Clean	`COc1cc(/C=C\C(=O)O)cc(OC)c1O`
ZINC156089	0.676	236.2 Da LogP 1.72 TPSA 72.8	✓ Ro5	✓ Clean	`COc1cc(/C=C/C(=O)O)ccc1OC(C)=O`

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.