Protein profile

VK055_3689

pimelyl-[acyl-carrier protein] methyl ester esterase

Genome: KpATCC43816

Gene: AIK82244.1 bioH Structure source: Experimental + ColabFold UniProt A6TF35

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Amino acids 257

Annotations 2

Features 12

PDB binders 9

Druggability 0.553

Overview

Basic information about this protein and its source genome.

Accession: VK055_3689
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK82244.1 bioH
Status: annotated
Amino acids: 257
Structure source: Experimental + ColabFold

GO:0052689 Catalysis of the hydrolysis of a carboxylic ester bond. GO:0009102 The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 30.172
Human E-value: 2.3e-06
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 33.168
Localization: Cytoplasmic
ColabFold pLDDT: 95.05

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 0.553

Structure 6K5E

Pocket Pocket 10

P2Rank 0.05

Structure 6K5E

Pocket Pocket 1

ColabFold model

FPocket 0.44 · Pocket 4

P2Rank 0.095 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 124 / 4744 genomes with a hit

Normalized 0.026

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0052689 Catalysis of the hydrolysis of a carboxylic ester bond.
GO:0009102 The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
4	254	SUPERFAMILY	SSF53474	alpha/beta-Hydrolases
4	254	InterPro	IPR029058	Alpha/Beta hydrolase fold
1	253	Gene3D	G3DSA:3.40.50.1820	alpha/beta hydrolase
1	253	InterPro	IPR029058	Alpha/Beta hydrolase fold
10	252	NCBIfam	TIGR01738	pimeloyl-ACP methyl ester esterase BioH
10	252	InterPro	IPR010076	Pimeloyl-[acyl-carrier protein] methyl ester esterase
13	250	PANTHER	PTHR43194	HYDROLASE ALPHA/BETA FOLD FAMILY
15	241	Pfam	PF00561	alpha/beta hydrolase fold
15	241	InterPro	IPR000073	Alpha/beta hydrolase fold-1
4	254	Hamap	MF_01260	Pimeloyl-[acyl-carrier protein] methyl ester esterase [bioH].
4	254	InterPro	IPR010076	Pimeloyl-[acyl-carrier protein] methyl ester esterase
1	255	FunFam	G3DSA:3.40.50.1820:FF:000045	Pimeloyl-[acyl-carrier protein] methyl ester esterase

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 6K5E	X-ray	20.00 Å	-	—	PDBe RCSB PDBj File	Viewing
ColabFold VK055_3689	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
93				0.821
102				0.585
85				0.335

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	28.74	0.927
2	22.64	0.882
3	12.98	0.67
4	10.78	0.579
5	10.3	0.553

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				0.44

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				2.96	0.096

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.

59 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
3OH	1M33	P13001	90.1 Da LogP -0.55 TPSA 57.5	✓ Ro5	✓ Clean	`C(CO)C(=O)O`
EEE	3HEA	P22862	88.1 Da LogP 0.57 TPSA 26.3	✓ Ro5	✓ Clean	`CCOC(=O)C`
EGC	5Z95	A0A0M3PNA2	602.8 Da LogP 3.90 TPSA 103.3	1 viol.	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(cc1)OCCOCCOCCOCCOCCOCCOCC…`
FP6	7C8L	A0A0M3PNA2	99.1 Da LogP 0.24 TPSA 20.3	✓ Ro5	✓ Clean	`C1CCN(C1)C=O`
J6Z	3IA2	P22862	137.2 Da LogP 0.33 TPSA 57.2	✓ Ro5	✓ Clean	`CC[C@@H](C)S(=O)(=O)[O-]`
PE3	5CBK	A0A0M5I297	634.8 Da LogP -0.81 TPSA 160.5	2 viol.	✓ Clean	`C(COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO)O`
PEO	3T52	P22862	34.0 Da LogP 0.02 TPSA 40.5	✓ Ro5	✓ Clean	`OO`
TZU	8DVC	A0A0M5I297	300.3 Da LogP 1.92 TPSA 61.8	✓ Ro5	✓ Clean	`CC1=C[C@@H](OC1=O)OC[C@H]2[C@H]3Cc4ccccc4[C@H]3…`
ZMK	4ETW	Q83PW0	514.5 Da LogP 0.49 TPSA 188.6	1 viol.	✓ Clean	`CC(C)(COP(=O)(O)O)[C@@H](C(=O)NCCC(=O)NCCSC(=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
ZINC2030966	1.000	294.4 Da LogP 3.79 TPSA 38.7	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCCO)cc1`
ZINC1532311	0.818	250.4 Da LogP 3.77 TPSA 29.5	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCO)cc1`
ZINC35650209	0.722	278.4 Da LogP 4.55 TPSA 29.5	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCCCO)cc1`
ZINC1592053	0.692	321.5 Da LogP 4.36 TPSA 21.7	✓ Ro5	✓ Clean	`CN(C)CCOCCOc1ccc(C(C)(C)CC(C)(C)C)cc1`
ZINC115086873	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1857792028	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC77271182	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC167273021	0.675	308.4 Da LogP 3.88 TPSA 55.8	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCC(=O)O)cc1`
ZINC4353076	0.651	352.5 Da LogP 4.42 TPSA 68.3	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCCSC(=N)N)cc1`
ZINC144169243	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC575441396	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC226069334	0.628	366.6 Da LogP 3.86 TPSA 38.7	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOC[C@@H](O)C[N+](C)(C)…`
ZINC226069348	0.628	366.6 Da LogP 3.86 TPSA 38.7	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOC[C@H](O)C[N+](C)(C)C…`
ZINC3844447	0.625	286.3 Da LogP 0.46 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOc1ccc(OCCOCCO)cc1`
ZINC1688152	0.609	380.5 Da LogP 3.96 TPSA 55.8	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCC[N+](C)(C)CC(=O)O)c…`
ZINC90741418	0.606	242.3 Da LogP 0.45 TPSA 68.2	✓ Ro5	✓ Clean	`OCCOCCOc1ccc(OCCO)cc1`
ZINC167715346	0.600	266.3 Da LogP -0.18 TPSA 77.4	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCOCCCO`
ZINC34160867	0.600	222.3 Da LogP -0.20 TPSA 68.2	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCCO`
ZINC1600251	0.595	208.3 Da LogP 2.75 TPSA 29.5	✓ Ro5	✓ Clean	`CCC(C)(C)c1ccc(OCCO)cc1`
ZINC1580159	0.588	210.3 Da LogP -0.26 TPSA 58.9	✓ Ro5	✓ Clean	`OCCOCCSCCOCCO`
ZINC32011214	0.587	363.5 Da LogP 4.13 TPSA 30.9	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCCN2CCOCC2)cc1`
ZINC1648298	0.579	206.2 Da LogP -1.17 TPSA 93.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@@H](O)[C@H](O)C(=O)OCC`
ZINC1648299	0.579	206.2 Da LogP -1.17 TPSA 93.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@H](O)[C@@H](O)C(=O)OCC`
ZINC1719698	0.579	250.2 Da LogP 2.94 TPSA 78.9	✓ Ro5	✓ Clean	`CCOC(=O)P(C(=O)OCC)C(=O)OCC`
ZINC17877781	0.579	206.2 Da LogP -1.17 TPSA 93.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@@H](O)[C@@H](O)C(=O)OCC`
ZINC258828116	0.579	452.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC258836919	0.579	364.4 Da LogP -0.27 TPSA 84.8	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38235275	0.579	200.2 Da LogP 1.45 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C(C)=C(/C)C(=O)OCC`
ZINC39200394	0.579	200.2 Da LogP 1.45 TPSA 52.6	✓ Ro5	✓ Clean	`CCOC(=O)/C(C)=C(\C)C(=O)OCC`
ZINC79016673	0.579	232.3 Da LogP -0.32 TPSA 57.2	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCO`
ZINC83254091	0.579	320.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCO`
ZINC96503366	0.579	408.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC96503406	0.579	276.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCO`
ZINC226069639	0.574	365.6 Da LogP 4.15 TPSA 50.7	✓ Ro5	✓ Clean	`CC(C)NC[C@@H](O)COCCOc1ccc(C(C)(C)CC(C)(C)C)cc1`
ZINC226069650	0.574	365.6 Da LogP 4.15 TPSA 50.7	✓ Ro5	✓ Clean	`CC(C)NC[C@H](O)COCCOc1ccc(C(C)(C)CC(C)(C)C)cc1`
ZINC16889914	0.558	308.5 Da LogP 4.41 TPSA 59.1	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCSC(=N)N)cc1`
ZINC140309458	0.556	438.5 Da LogP 3.15 TPSA 88.4	✓ Ro5	✓ Clean	`CC(c1ccc(OCCO)cc1)(c1ccc(OCCO)cc1)c1ccc(OCCO)cc1`
ZINC1531061	0.556	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCO`
ZINC1690586	0.556	316.4 Da LogP 2.75 TPSA 58.9	✓ Ro5	✓ Clean	`CC(C)(c1ccc(OCCO)cc1)c1ccc(OCCO)cc1`

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.