Protein profile

KP13_00594

Rhamnose ABC transporter, periplasmic rhamnose-binding protein

Genome: KpKP13

Gene: AHE47069.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GGA4

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Amino acids 328

Annotations 3

Features 17

PDB binders 4

Druggability 0.411

Overview

Basic information about this protein and its source genome.

Accession: KP13_00594
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE47069.1
Status: annotated
Amino acids: 328
Structure source: AlphaFold + ColabFold

GO:0015762 The process in which rhamnose is transported across a lipid bilayer, from one side of a membrane to the other. Rhamnose occurs commonly as a compound of plant glycosides, in polysaccharides of gums and mucilages, and in bacterial polysaccharides. It is also a component of some plant cell wall polysaccharides and frequently acts as the sugar components of flavonoids. GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall. GO:0030246 Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.

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: Periplasmic
ColabFold pLDDT: 94.57

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 0.411

Structure A0A0H3GGA4

Pocket Pocket 1

P2Rank 0.428

Structure A0A0H3GGA4

Pocket Pocket 1

ColabFold model

FPocket 0.41 · Pocket 1

P2Rank 0.556 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 30 / 4744 genomes with a hit

Normalized 0.006

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0015762 The process in which rhamnose is transported across a lipid bilayer, from one side of a membrane to the other. Rhamnose occurs commonly as a compound of plant glycosides, in polysaccharides of gums and mucilages, and in bacterial polysaccharides. It is also a component of some plant cell wall polysaccharides and frequently acts as the sugar components of flavonoids.
GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
GO:0030246 Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
25	310	Gene3D	G3DSA:3.40.50.2300	-
7	324	PANTHER	PTHR30036	D-XYLOSE-BINDING PERIPLASMIC PROTEIN
1	5	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	22	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
127	324	Gene3D	G3DSA:3.40.50.2300	-
6	17	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	22	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
26	326	NCBIfam	TIGR02637	rhamnose ABC transporter substrate-binding protein
26	326	InterPro	IPR013459	Rhamnose ABC transporter, substrate-binding protein RhaS
18	22	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
23	328	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
7	29	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
26	286	Pfam	PF13407	Periplasmic binding protein domain
26	286	InterPro	IPR025997	Periplasmic binding protein
1	22	Phobius	SIGNAL_PEPTIDE	Signal peptide region
23	324	SUPERFAMILY	SSF53822	Periplasmic binding protein-like I
23	324	InterPro	IPR028082	Periplasmic binding protein-like I

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_A0A0H3GGA4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00594	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				0.411

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	6.96	0.359
2	3.83	0.149
3	1.07	0.007

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				0.41

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	8.36	0.446
2	3.07	0.102
3	1.0	0.005

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.

54 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
BDR	3KSM	Q2S7D2	150.1 Da LogP -2.58 TPSA 90.2	✓ Ro5	✓ Clean	`C([C@@H]1[C@H]([C@H]([C@@H](O1)O)O)O)O`
LTH	4PE6	D6Y8L8	136.1 Da LogP -2.21 TPSA 98.0	✓ Ro5	✓ Clean	`C([C@@H]([C@H](C(=O)O)O)O)O`
PAV	4PZ0	A0A6H3AKG3	150.1 Da LogP -2.23 TPSA 90.2	✓ Ro5	✓ Clean	`C[C@@]1(C([C@H](CO1)O)(O)O)O`
RIP	4ZJP	A6VKT0	150.1 Da LogP -2.58 TPSA 90.2	✓ Ro5	✓ Clean	`C1[C@H]([C@H]([C@H]([C@@H](O1)O)O)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).

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
ZINC11592819	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC11592820	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)…`
ZINC11592821	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O…`
ZINC1531006	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O…`
ZINC1531007	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)…`
ZINC33991088	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H]…`
ZINC34049524	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)[C@@H](O…`
ZINC34370883	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](…`
ZINC4403706	0.636	256.2 Da LogP -4.77 TPSA 178.9	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H…`
ZINC4403707	0.636	256.2 Da LogP -4.77 TPSA 178.9	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H…`
ZINC4403708	0.636	256.2 Da LogP -4.77 TPSA 178.9	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H]…`
ZINC4403709	0.636	256.2 Da LogP -4.77 TPSA 178.9	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H]…`
ZINC4521295	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H…`
ZINC4521296	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H]…`
ZINC4521297	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H]…`
ZINC4521298	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](…`
ZINC5830322	0.636	226.2 Da LogP -4.13 TPSA 158.7	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)…`
ZINC104251170	0.600	207.2 Da LogP -2.65 TPSA 93.4	✓ Ro5	✓ Clean	`CN(C)[C@@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC203488208	0.600	207.2 Da LogP -2.65 TPSA 93.4	✓ Ro5	✓ Clean	`CN(C)[C@@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC257346191	0.600	207.2 Da LogP -2.65 TPSA 93.4	✓ Ro5	✓ Clean	`CN(C)[C@H]1[C@H](O)[C@@H](O)[C@@H](CO)O[C@H]1O`
ZINC257346192	0.600	207.2 Da LogP -2.65 TPSA 93.4	✓ Ro5	✓ Clean	`CN(C)[C@H]1[C@H](O)[C@H](O)[C@@H](CO)O[C@H]1O`
ZINC100352116	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@H…`
ZINC101411480	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@H]…`
ZINC12358758	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@@H]2[C@@H](CO)O[C@@H](O)[C@…`
ZINC13536670	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@@H]2[C@@H](CO)O[C@H](O)[C@@…`
ZINC13543975	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@@H]2[C@@H](CO)O[C@@H](O)[C@…`
ZINC13549339	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@H]1O[C@@H…`
ZINC1857776274	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@@H]2O[C@H](O)[C@@H](O)[C@H]…`
ZINC1857776275	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@@H]2O[C@H](O)[C@@H](O)[C@@H…`
ZINC202563257	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@H…`
ZINC245204744	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O[C@@H]2[C@H](CO)O[C@H](O)[C@H…`
ZINC245204745	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@H…`
ZINC253615779	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](OC[C@@H]2O[C@H](O)[C@H](O)[C@H]…`
ZINC26892042	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@@H]1O[C@…`
ZINC33821316	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@H]2[C@@H](CO)O[C@@H](O)[C@H]…`
ZINC35262677	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@…`
ZINC3978744	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@@H]2[C@@H](CO)O[C@H](O)[C@H…`
ZINC4095762	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O)[C@H…`
ZINC4095793	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O[C@@H…`
ZINC4096703	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@H]2O[C@@H](O)[C@H](O)[C@@H]…`
ZINC4097113	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@@H]2[C@@H](CO)O[C@@H](O)[C@…`
ZINC43505220	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@H]1O[C@H]…`
ZINC43943076	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@@H]1O[C@@…`
ZINC5222455	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@H]1O[C@H]…`
ZINC575127214	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](OC[C@@H]2O[C@H](O)[C@H](O)[C@@H…`
ZINC575127215	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](OC[C@@H]2O[C@H](O)[C@H](O)[C@@H…`
ZINC599389313	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@H]1O[C@H]…`
ZINC613838159	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](OC[C@@H]2O[C@H](O)[C@H](O)[C@@H…`
ZINC72283165	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@@H]2[C@H](CO)O[C@H](O)[C@H]…`
ZINC88466429	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](OC[C@H]2O[C@H](O)[C@H](O)[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.