Protein profile

VK055_1822

esterase ybfF

Genome: KpATCC43816

Gene: ybfF AIK80435.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GK08

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Amino acids 257

Annotations 1

Features 8

PDB binders 1

Druggability 0.315

Overview

Basic information about this protein and its source genome.

Accession: VK055_1822
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: ybfF AIK80435.1
Status: annotated
Amino acids: 257
Structure source: AlphaFold + ColabFold

GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 45.122
Human E-value: 6.01e-15
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 40.0
Localization: Unknown
ColabFold pLDDT: 97.55

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 0.315

Structure A0A0H3GK08

Pocket Pocket 13

P2Rank 0.8

Structure A0A0H3GK08

Pocket Pocket 1

ColabFold model

FPocket 0.692 · Pocket 4

P2Rank 0.681 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 114 / 4744 genomes with a hit

Normalized 0.024

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.

Sequence Features

Domain/signature hits from InterPro and related databases.

8 records

Show feature table

Start	End	DB	Term	Name
7	253	FunFam	G3DSA:3.40.50.1820:FF:000039	Esterase ybfF
19	246	Pfam	PF12697	Alpha/beta hydrolase family
19	246	InterPro	IPR000073	Alpha/beta hydrolase fold-1
12	252	SUPERFAMILY	SSF53474	alpha/beta-Hydrolases
12	252	InterPro	IPR029058	Alpha/Beta hydrolase fold
2	254	PANTHER	PTHR46118	PROTEIN ABHD11
1	253	Gene3D	G3DSA:3.40.50.1820	alpha/beta hydrolase
1	253	InterPro	IPR029058	Alpha/Beta hydrolase 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_A0A0H3GK08	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_1822	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
3				0.104
2				0.005
4				0.002
1				0.001

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	20.86	0.8
2	6.63	0.283
3	3.35	0.094
4	1.75	0.026

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
4				0.692
10				0.051
1				0.019
3				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	15.78	0.681
2	7.59	0.336
3	5.31	0.205
4	3.2	0.087
5	2.05	0.038

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.

41 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
MLA	3BF8	P75736	104.1 Da LogP -0.45 TPSA 74.6	✓ Ro5	✓ Clean	`C(C(=O)O)C(=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
CHEMBL1490250	Q8K4F5	—	232.2 Da LogP 0.73 TPSA 60.2	✓ Ro5	✓ Clean	`O=C(N1CCOCC1)n1nnc2ccccc21`
CHEMBL1869321	Q8K4F5	—	406.5 Da LogP 3.03 TPSA 80.5	✓ Ro5	✓ Clean	`COCC1CCCCN1C(=O)n1ncc(C(O)(c2ccccc2)c2ccccc2)n1`
CHEMBL1891894	Q8K4F5	—	390.5 Da LogP 3.79 TPSA 71.2	✓ Ro5	✓ Clean	`CCC1CCCCN1C(=O)n1ncc(C(O)(c2ccccc2)c2ccccc2)n1`
CHEMBL1903566	Q8K4F5	—	418.5 Da LogP 4.29 TPSA 71.2	✓ Ro5	✓ Clean	`CC(C)(C)C1CCN(C(=O)n2ncc(C(O)(c3ccccc3)c3ccccc3…`

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
ZINC152138	1.000	232.2 Da LogP 0.73 TPSA 60.2	✓ Ro5	✓ Clean	`O=C(N1CCOCC1)n1nnc2ccccc21`
ZINC72138441	1.000	390.5 Da LogP 3.79 TPSA 71.2	✓ Ro5	✓ Clean	`CC[C@@H]1CCCCN1C(=O)n1ncc(C(O)(c2ccccc2)c2ccccc…`
ZINC72138442	1.000	390.5 Da LogP 3.79 TPSA 71.2	✓ Ro5	✓ Clean	`CC[C@H]1CCCCN1C(=O)n1ncc(C(O)(c2ccccc2)c2ccccc2…`
ZINC152140	0.737	230.3 Da LogP 1.89 TPSA 51.0	✓ Ro5	✓ Clean	`O=C(N1CCCCC1)n1nnc2ccccc21`
ZINC403334	0.657	264.2 Da LogP 1.69 TPSA 78.5	✓ Ro5	✓ Clean	`O=C(n1nnc2ccccc21)n1nnc2ccccc21`
ZINC4689604	0.628	246.3 Da LogP 0.29 TPSA 60.2	✓ Ro5	✓ Clean	`O=C(Cn1nnc2ccccc21)N1CCOCC1`
ZINC72136890	0.589	418.5 Da LogP 4.29 TPSA 71.2	✓ Ro5	✓ Clean	`CC(C)(C)C1CCN(C(=O)n2ncc(C(O)(c3ccccc3)c3ccccc3…`
ZINC9909791	0.587	262.3 Da LogP -0.28 TPSA 69.5	✓ Ro5	✓ Clean	`O=C(COn1nnc2ccccc21)N1CCOCC1`
ZINC292505	0.581	231.3 Da LogP 1.34 TPSA 47.4	✓ Ro5	✓ Clean	`O=C(N1CCOCC1)n1cnc2ccccc21`
ZINC783157	0.571	372.4 Da LogP 1.14 TPSA 94.4	✓ Ro5	✓ Clean	`O=C(c1ccc(S(=O)(=O)N2CCOCC2)cc1)n1nnc2ccccc21`
ZINC100314807	0.569	404.6 Da LogP 3.05 TPSA 86.3	✓ Ro5	✓ Clean	`O=[N+]([O-])/C(C(Cl)=C(Cl)Cl)=C(\N1CCOCC1)n1nnc…`
ZINC5694392	0.566	353.3 Da LogP 1.86 TPSA 103.4	✓ Ro5	Alert	`O=C(c1cc([N+](=O)[O-])ccc1N1CCOCC1)n1nnc2ccccc21`
ZINC4917214	0.538	372.4 Da LogP 1.14 TPSA 94.4	✓ Ro5	✓ Clean	`O=C(c1cccc(S(=O)(=O)N2CCOCC2)c1)n1nnc2ccccc21`
ZINC4904885	0.525	320.3 Da LogP 1.94 TPSA 95.6	✓ Ro5	✓ Clean	`O=C(CCC(=O)n1nnc2ccccc21)n1nnc2ccccc21`
ZINC676888	0.525	368.4 Da LogP 2.55 TPSA 95.6	✓ Ro5	✓ Clean	`O=C(c1ccc(C(=O)n2nnc3ccccc32)cc1)n1nnc2ccccc21`
ZINC15780050	0.524	232.3 Da LogP 1.66 TPSA 34.0	✓ Ro5	✓ Clean	`S=C(N1CCCC1)n1nnc2ccccc21`
ZINC101721	0.512	223.2 Da LogP 2.12 TPSA 47.8	✓ Ro5	✓ Clean	`O=C(c1ccccc1)n1nnc2ccccc21`
ZINC2566723	0.512	215.1 Da LogP 1.63 TPSA 47.8	✓ Ro5	✓ Clean	`O=C(n1nnc2ccccc21)C(F)(F)F`
ZINC15781247	0.512	246.3 Da LogP 2.05 TPSA 34.0	✓ Ro5	✓ Clean	`S=C(N1CCCCC1)n1nnc2ccccc21`
ZINC614517	0.511	268.3 Da LogP -0.14 TPSA 77.3	✓ Ro5	✓ Clean	`O=S(=O)(N1CCOCC1)n1nnc2ccccc21`
ZINC3306280	0.509	406.9 Da LogP 1.79 TPSA 94.4	✓ Ro5	✓ Clean	`O=C(c1ccc(Cl)c(S(=O)(=O)N2CCOCC2)c1)n1nnc2ccccc…`
ZINC138079998	0.500	212.0 Da LogP 1.41 TPSA 37.3	✓ Ro5	✓ Clean	`C=C(I)CC(=O)O`
ZINC152115	0.500	321.4 Da LogP 2.93 TPSA 47.4	✓ Ro5	✓ Clean	`O=C(N1CCOCC1)n1c(Cc2ccccc2)nc2ccccc21`
ZINC15782196	0.500	320.3 Da LogP 1.79 TPSA 95.6	✓ Ro5	✓ Clean	`CC(C(=O)n1nnc2ccccc21)C(=O)n1nnc2ccccc21`
ZINC19300942	0.500	218.3 Da LogP 0.72 TPSA 43.2	✓ Ro5	✓ Clean	`c1ccc2c(c1)nnn2CN1CCOCC1`
ZINC22015855	0.500	232.3 Da LogP 0.76 TPSA 43.2	✓ Ro5	✓ Clean	`c1ccc2c(c1)nnn2CCN1CCOCC1`
ZINC2378058	0.500	348.4 Da LogP 2.72 TPSA 95.6	✓ Ro5	✓ Clean	`O=C(CCCCC(=O)n1nnc2ccccc21)n1nnc2ccccc21`
ZINC2571471	0.500	203.2 Da LogP 2.12 TPSA 47.8	✓ Ro5	✓ Clean	`CC(C)(C)C(=O)n1nnc2ccccc21`
ZINC37022236	0.500	261.3 Da LogP 2.79 TPSA 57.6	✓ Ro5	✓ Clean	`CC[C@@H]1CCCCN1C(=O)c1ccccc1C(=O)O`
ZINC37022237	0.500	261.3 Da LogP 2.79 TPSA 57.6	✓ Ro5	✓ Clean	`CC[C@H]1CCCCN1C(=O)c1ccccc1C(=O)O`
ZINC46087949	0.500	244.3 Da LogP 0.50 TPSA 68.2	✓ Ro5	✓ Clean	`O=C(c1nnc2ccccc2n1)N1CCOCC1`
ZINC497102	0.500	280.3 Da LogP 1.86 TPSA 61.4	✓ Ro5	✓ Clean	`S=C(n1nnc2ccccc21)n1nnc2ccccc21`
ZINC5283944	0.500	217.3 Da LogP 2.51 TPSA 47.8	✓ Ro5	✓ Clean	`CC(C)(C)CC(=O)n1nnc2ccccc21`
ZINC5771119	0.500	239.2 Da LogP 1.83 TPSA 68.0	✓ Ro5	✓ Clean	`O=C(c1ccccc1O)n1nnc2ccccc21`
ZINC58342982	0.500	295.4 Da LogP 3.55 TPSA 46.1	✓ Ro5	✓ Clean	`CC[C@@H]1CCCCN1C(=O)c1cnc(-c2ccccc2)nc1`
ZINC58342983	0.500	295.4 Da LogP 3.55 TPSA 46.1	✓ Ro5	✓ Clean	`CC[C@H]1CCCCN1C(=O)c1cnc(-c2ccccc2)nc1`

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.