Protein profile

KP13_03367

D-ribose-binding protein

Genome: KpKP13

Gene: AHE45746.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GPU0

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Amino acids 345

Annotations 3

Features 14

PDB binders 5

Druggability 0.66

Overview

Basic information about this protein and its source genome.

Accession: KP13_03367
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45746.1
Status: annotated
Amino acids: 345
Structure source: AlphaFold + ColabFold

GO:0030313 An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present. 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. GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

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: 90.14

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 0.66

Structure A0A0H3GPU0

Pocket Pocket 1

P2Rank 0.855

Structure A0A0H3GPU0

Pocket Pocket 1

ColabFold model

FPocket 0.615 · Pocket 1

P2Rank 0.783 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 9 / 4744 genomes with a hit

Normalized 0.002

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0030313 An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present.
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.
GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
151	296	Gene3D	G3DSA:3.40.50.2300	-
51	324	SUPERFAMILY	SSF53822	Periplasmic binding protein-like I
51	324	InterPro	IPR028082	Periplasmic binding protein-like I
38	43	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
33	326	PANTHER	PTHR46847	D-ALLOSE-BINDING PERIPLASMIC PROTEIN-RELATED
54	314	Pfam	PF13407	Periplasmic binding protein domain
54	314	InterPro	IPR025997	Periplasmic binding protein
1	43	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
26	37	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
73	318	Gene3D	G3DSA:3.40.50.2300	-
53	326	CDD	cd06305	PBP1_methylthioribose_binding-like
1	43	Phobius	SIGNAL_PEPTIDE	Signal peptide region
44	345	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	25	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.

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_A0A0H3GPU0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03367	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				0.66

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				19.43	0.839

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				0.615

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				15.3	0.751
2				0.59	0.0

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.

55 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
3VB	4RSM	A0QYB5	122.1 Da LogP -2.31 TPSA 80.9	✓ Ro5	✓ Clean	`C([C@H]([C@@H](CO)O)O)O`
62W	5HKO	A0QYB3	182.2 Da LogP -3.59 TPSA 121.4	1 viol.	✓ Clean	`C([C@H]([C@@H]([C@H]([C@H](CO)O)O)O)O)O`
GZL	2VK2	P39325	180.2 Da LogP -3.22 TPSA 110.4	✓ Ro5	✓ Clean	`C(C([C@H]1C(C([C@@H](O1)O)O)O)O)O`
RIP	7E7M	Q8E283	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`
X9X	4WT7	B9K0E0	182.2 Da LogP -3.59 TPSA 121.4	1 viol.	✓ Clean	`C([C@H]([C@H]([C@H]([C@H](CO)O)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
ZINC15657695	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@…`
ZINC25721048	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C…`
ZINC25721054	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC4726901	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@H](O)[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@…`
ZINC4726902	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C…`
ZINC4726903	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C…`
ZINC4726904	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[…`
ZINC100055463	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC100064885	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC17780060	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC17952732	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC18042331	0.917	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H]…`
ZINC18120313	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC3979006	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC4403103	0.917	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC4403105	0.917	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC4403107	0.917	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@…`
ZINC9212412	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@@H](O)CO`
ZINC5201837	0.647	345.3 Da LogP -6.55 TPSA 214.3	2 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@H](…`
ZINC5201838	0.647	345.3 Da LogP -6.55 TPSA 214.3	2 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@@H]…`
ZINC5201839	0.647	345.3 Da LogP -6.55 TPSA 214.3	2 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@H](…`
ZINC5201841	0.647	345.3 Da LogP -6.55 TPSA 214.3	2 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@@H]…`
ZINC101356848	0.579	388.4 Da LogP -6.96 TPSA 226.4	2 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)CNCCNC[C@H](O…`
ZINC215968865	0.579	388.4 Da LogP -6.96 TPSA 226.4	2 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)CNCCNC[C@H](O…`
ZINC215968917	0.579	388.4 Da LogP -6.96 TPSA 226.4	2 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)CNCCNC[C@H](O…`
ZINC215968963	0.579	388.4 Da LogP -6.96 TPSA 226.4	2 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CNCCNC[C@@H…`
ZINC216185927	0.579	209.2 Da LogP -3.02 TPSA 104.4	✓ Ro5	✓ Clean	`CN(C)C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC216185976	0.579	209.2 Da LogP -3.02 TPSA 104.4	✓ Ro5	✓ Clean	`CN(C)C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC216186168	0.579	224.3 Da LogP -2.87 TPSA 101.2	✓ Ro5	✓ Clean	`C[N+](C)(C)C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC216186206	0.579	224.3 Da LogP -2.87 TPSA 101.2	✓ Ro5	✓ Clean	`C[N+](C)(C)C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC25624721	0.579	209.2 Da LogP -3.02 TPSA 104.4	✓ Ro5	✓ Clean	`CN(C)C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC25624980	0.579	224.3 Da LogP -2.87 TPSA 101.2	✓ Ro5	✓ Clean	`C[N+](C)(C)C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC4566610	0.579	209.2 Da LogP -3.02 TPSA 104.4	✓ Ro5	✓ Clean	`CN(C)C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC4566614	0.579	224.3 Da LogP -2.87 TPSA 101.2	✓ Ro5	✓ Clean	`C[N+](C)(C)C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC255980408	0.577	414.4 Da LogP -5.66 TPSA 208.0	2 viol.	✓ Clean	`O[C@H]1OC[C@@H](O[C@H]2OC[C@@H](O[C@H]3OC[C@@H]…`
ZINC255980409	0.577	414.4 Da LogP -5.66 TPSA 208.0	2 viol.	✓ Clean	`O[C@H]1OC[C@@H](O[C@H]2OC[C@@H](O[C@H]3OC[C@@H]…`
ZINC255980410	0.577	414.4 Da LogP -5.66 TPSA 208.0	2 viol.	✓ Clean	`O[C@@H]1[C@H](O)[C@@H](O[C@@H]2CO[C@H](O[C@@H]3…`
ZINC255980411	0.577	414.4 Da LogP -5.66 TPSA 208.0	2 viol.	✓ Clean	`O[C@H]1OC[C@@H](O[C@H]2OC[C@@H](O[C@H]3OC[C@@H]…`
ZINC263584059	0.577	414.4 Da LogP -5.66 TPSA 208.0	2 viol.	✓ Clean	`O[C@@H]1[C@@H](O[C@@H]2OC[C@@H](O)[C@H](O)[C@H]…`
ZINC263584060	0.577	414.4 Da LogP -5.66 TPSA 208.0	2 viol.	✓ Clean	`O[C@H]1[C@H](O)[C@@H](O[C@@H]2CO[C@@H](O)[C@H](…`
ZINC263584061	0.577	414.4 Da LogP -5.66 TPSA 208.0	2 viol.	✓ Clean	`O[C@@H]1[C@@H](O[C@H]2OC[C@@H](O)[C@H](O)[C@H]2…`
ZINC4095690	0.577	282.2 Da LogP -4.12 TPSA 149.1	1 viol.	✓ Clean	`O[C@H]1[C@H](O)CO[C@@H](O[C@@H]2CO[C@H](O)[C@H]…`
ZINC4095691	0.577	282.2 Da LogP -4.12 TPSA 149.1	1 viol.	✓ Clean	`O[C@H]1[C@H](O)CO[C@@H](O[C@@H]2CO[C@@H](O)[C@H…`
ZINC64622127	0.577	414.4 Da LogP -5.66 TPSA 208.0	2 viol.	✓ Clean	`O[C@H]1[C@H](O)CO[C@@H](O[C@@H]2CO[C@@H](O[C@@H…`
ZINC78590548	0.577	414.4 Da LogP -5.66 TPSA 208.0	2 viol.	✓ Clean	`O[C@H]1[C@H](O)CO[C@@H](O[C@@H]2CO[C@@H](O[C@@H…`
ZINC85546060	0.577	414.4 Da LogP -5.66 TPSA 208.0	2 viol.	✓ Clean	`O[C@H]1[C@H](O)[C@@H](O[C@@H]2CO[C@@H](O)[C@H](…`
ZINC12953159	0.550	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC12953168	0.550	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC4353167	0.550	240.2 Da LogP -4.66 TPSA 158.7	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O…`
ZINC5830322	0.550	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)…`

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.