Protein profile

VK055_0661

bacterial alpha-L-rhamnosidase family protein

Genome: KpATCC43816

Gene: AIK79284.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GY38

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Amino acids 870

Annotations 3

Features 16

PDB binders 1

Druggability 0.886

Overview

Basic information about this protein and its source genome.

Accession: VK055_0661
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79284.1
Status: annotated
Amino acids: 870
Structure source: AlphaFold + ColabFold

3.2.1.40

GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0030596 Catalysis of the hydrolysis of terminal non-reducing alpha-L-rhamnose residues in alpha-L-rhamnosides.

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: Cytoplasmic
ColabFold pLDDT: 95.1

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 0.886

Structure A0A0H3GY38

Pocket Pocket 1

P2Rank 0.924

Structure A0A0H3GY38

Pocket Pocket 1

ColabFold model

FPocket 0.506 · Pocket 5

P2Rank 0.895 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 1 / 4744 genomes with a hit

Normalized 0

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Enzyme Commission (EC)

3.2.1.40

Gene Ontology (GO)

GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
GO:0030596 Catalysis of the hydrolysis of terminal non-reducing alpha-L-rhamnose residues in alpha-L-rhamnosides.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
774	845	Gene3D	G3DSA:2.60.420.10	Maltose phosphorylase, domain 3
51	839	PANTHER	PTHR33307	ALPHA-RHAMNOSIDASE (EUROFUNG)
782	837	Pfam	PF17390	Bacterial alpha-L-rhamnosidase C-terminal domain
782	837	InterPro	IPR035398	Alpha-L-rhamnosidase C-terminal domain
435	838	SUPERFAMILY	SSF48208	Six-hairpin glycosidases
435	838	InterPro	IPR008928	Six-hairpin glycosidase superfamily
297	433	Gene3D	G3DSA:2.60.120.260	-
436	767	Pfam	PF17389	Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain
436	767	InterPro	IPR035396	Alpha-L-rhamnosidase, six-hairpin glycosidase domain
133	297	Pfam	PF08531	Alpha-L-rhamnosidase N-terminal domain
133	297	InterPro	IPR013737	Bacterial alpha-L-rhamnosidase N-terminal
436	770	Gene3D	G3DSA:1.50.10.10	-
436	770	InterPro	IPR012341	Six-hairpin glycosidase-like superfamily
312	430	Pfam	PF05592	Bacterial alpha-L-rhamnosidase concanavalin-like domain
312	430	InterPro	IPR008902	Alpha-L-rhamnosidase, concanavalin-like domain
93	286	Gene3D	G3DSA:2.60.120.260	-

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_A0A0H3GY38	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0661	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				0.886
4				0.316
2				0.243

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	27.01	0.918
2	9.08	0.486
3	8.47	0.452
4	5.58	0.267
5	5.47	0.26

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				0.506
1				0.333
3				0.272

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	22.4	0.88
2	12.41	0.65
3	5.81	0.284
4	5.38	0.255
5	5.18	0.24

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.

51 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
AE3	6I60	B5YC64	134.2 Da LogP 0.03 TPSA 38.7	✓ Ro5	✓ Clean	`CCOCCOCCO`

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
ZINC5650743	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
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`
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`
ZINC5859031	0.688	294.4 Da LogP 1.13 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCC`
ZINC1644613	0.619	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC1580161	0.600	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.600	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.600	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.600	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	0.600	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.600	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	0.600	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC2555269	0.591	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
ZINC4974293	0.579	280.4 Da LogP 1.08 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCOCCOCCOCC`
ZINC100014200	0.565	494.7 Da LogP 4.02 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC100070166	0.565	290.4 Da LogP 3.17 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCO`
ZINC100310628	0.565	478.7 Da LogP 4.78 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC100365196	0.565	302.5 Da LogP 4.71 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCO`
ZINC101772322	0.565	434.7 Da LogP 4.76 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC103600921	0.565	466.7 Da LogP 3.24 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC14880431	0.565	378.6 Da LogP 3.20 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC14881140	0.565	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
ZINC16051619	0.565	350.5 Da LogP 2.42 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCOCCO`
ZINC2584424	0.565	218.3 Da LogP 2.37 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCO`
ZINC4521877	0.565	234.3 Da LogP 1.61 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCO`
ZINC5273610	0.565	322.4 Da LogP 1.64 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCOCCOCCO`
ZINC58538366	0.565	392.6 Da LogP 3.59 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC58631420	0.565	422.6 Da LogP 3.22 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC59441819	0.565	318.5 Da LogP 3.95 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCO`
ZINC59622400	0.565	274.4 Da LogP 3.93 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCO`
ZINC71788551	0.565	334.5 Da LogP 3.19 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCO`
ZINC71788564	0.565	262.4 Da LogP 2.39 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCO`
ZINC71788567	0.565	406.6 Da LogP 3.98 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC8214594	0.565	362.6 Da LogP 3.97 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC88260008	0.565	390.6 Da LogP 4.75 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC95784968	0.565	450.7 Da LogP 4.00 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC95863931	0.565	464.7 Da LogP 4.39 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC116078620	0.538	236.3 Da LogP -0.41 TPSA 74.2	✓ Ro5	✓ Clean	`CCOC(=O)COCCOCCOCCO`
ZINC83253955	0.538	206.2 Da LogP -0.03 TPSA 65.0	✓ Ro5	✓ Clean	`CCOC(=O)CCOCCOCCO`
ZINC137432264	0.524	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823	0.524	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442	0.524	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028	0.524	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776	0.524	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446	0.524	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`

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.