Protein profile

KP13_02261

Putative ABC transporter substrate-binding protein

Genome: KpKP13

Gene: AHE42833.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GX53

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Amino acids 428

Annotations 1

Features 13

PDB binders 1

Druggability 0.363

Overview

Basic information about this protein and its source genome.

Accession: KP13_02261
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42833.1
Status: annotated
Amino acids: 428
Structure source: AlphaFold + ColabFold

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.

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: Unknown
ColabFold pLDDT: 94.14

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 0.363

Structure A0A0H3GX53

Pocket Pocket 6

P2Rank 0.949

Structure A0A0H3GX53

Pocket Pocket 1

ColabFold model

FPocket 0.991 · Pocket 1

P2Rank 0.952 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 42 / 4744 genomes with a hit

Normalized 0.009

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

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.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
4	344	PANTHER	PTHR43649	ARABINOSE-BINDING PROTEIN-RELATED
1	23	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
24	423	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	23	Phobius	SIGNAL_PEPTIDE	Signal peptide region
28	371	Gene3D	G3DSA:3.40.190.10	-
24	428	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
16	23	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
45	331	Pfam	PF01547	Bacterial extracellular solute-binding protein
45	331	InterPro	IPR006059	Bacterial extracellular solute-binding protein
4	15	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	23	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
137	415	Gene3D	G3DSA:3.40.190.10	-

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_A0A0H3GX53	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02261	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
6				0.363

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	28.42	0.925
2	1.83	0.035
3	1.27	0.013

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				0.991
11				0.319

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	28.03	0.923
2	3.18	0.109
3	1.41	0.018

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
TXT	3K02	B0B0V1	809.8 Da LogP -10.66 TPSA 400.3	3 viol.	✓ Clean	`C[C@@H]1[C@H]([C@H]([C@H]([C@H](O1)O[C@@H]2[C@H…`

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
ZINC100055151	0.569	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@H](O[C@H]2[C@H](O[C@@H]3[C@@H](CO)O…`
ZINC100055153	0.569	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@H](O[C@H]2[C@H](O[C@@H]3[C@@H](CO)O…`
ZINC100055156	0.569	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](CO)O[C@@H…`
ZINC100055157	0.569	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](CO)O[C@@H…`
ZINC2362797719	0.569	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@@H](O[C@H]2[C@H](O[C@H]3[C@@H](O)[C…`
ZINC55537584	0.569	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@@H](O[C@H]2[C@H](O[C@@H]3[C@@H](CO)…`
ZINC103664702	0.549	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@@H](O)O[C@H…`
ZINC103664705	0.549	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@H](O)O[C@H]…`
ZINC100352116	0.532	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…`
ZINC12358840	0.532	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…`
ZINC13542690	0.532	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…`
ZINC13543637	0.532	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]…`
ZINC13544017	0.532	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](…`
ZINC13544387	0.532	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	0.532	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…`
ZINC16051576	0.532	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…`
ZINC169619623	0.532	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…`
ZINC1857777749	0.532	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…`
ZINC1857777750	0.532	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@…`
ZINC202563257	0.532	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…`
ZINC21984931	0.532	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@@…`
ZINC2382416917	0.532	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@@…`
ZINC2382416919	0.532	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@@…`
ZINC2383776696	0.532	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…`
ZINC2383776697	0.532	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…`
ZINC238735529	0.532	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@…`
ZINC238809271	0.532	990.9 Da LogP -14.10 TPSA 506.1	3 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@H](O[C@@H]…`
ZINC242495944	0.532	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]…`
ZINC257362198	0.532	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]…`
ZINC257362199	0.532	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]…`
ZINC26892042	0.532	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@…`
ZINC35262676	0.532	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@@…`
ZINC35262677	0.532	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@@…`
ZINC3830982	0.532	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…`
ZINC3830983	0.532	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…`
ZINC3830985	0.532	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…`
ZINC38599727	0.532	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]…`
ZINC38599730	0.532	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]…`
ZINC38599734	0.532	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]…`
ZINC38792149	0.532	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]…`
ZINC4095490	0.532	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	0.532	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…`
ZINC4261771	0.532	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@@…`
ZINC4261772	0.532	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@@…`
ZINC44185569	0.532	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…`
ZINC5222455	0.532	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]…`
ZINC5222464	0.532	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…`
ZINC599389315	0.532	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]…`
ZINC72283166	0.532	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]…`
ZINC72283167	0.532	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]…`

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.