Protein profile

KP13_09592

Leucine-specific-binding protein

Genome: KpKP13

Gene: livK ANJ86568.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GZM8

Export view

Amino acids 369

Annotations 3

Features 30

PDB binders 1

Druggability 0.385

Overview

Basic information about this protein and its source genome.

Accession: KP13_09592
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: livK ANJ86568.1
Status: annotated
Amino acids: 369
Structure source: AlphaFold + ColabFold

GO:0006865 The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. 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:0015820 The directed movement of L-leucine, 2-amino-4-methylpentanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

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: 94.65

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 0.385

Structure A0A0H3GZM8

Pocket Pocket 4

P2Rank 0.079

Structure A0A0H3GZM8

Pocket Pocket 1

ColabFold model

FPocket 0.184 · Pocket 16

P2Rank 0.125 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 120 / 4744 genomes with a hit

Normalized 0.025

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0006865 The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
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:0015820 The directed movement of L-leucine, 2-amino-4-methylpentanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records

Show feature table

Start	End	DB	Term	Name
1	23	SignalP_EUK	SignalP-noTM	SignalP-noTM
1	23	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
144	272	FunFam	G3DSA:3.40.50.2300:FF:000033	Amino acid ABC transporter substrate-binding protein
27	343	Gene3D	G3DSA:3.40.50.2300	-
1	23	Phobius	SIGNAL_PEPTIDE	Signal peptide region
3	368	PANTHER	PTHR47151	LEU/ILE/VAL-BINDING ABC TRANSPORTER SUBUNIT
24	363	SUPERFAMILY	SSF53822	Periplasmic binding protein-like I
24	363	InterPro	IPR028082	Periplasmic binding protein-like I
1	6	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
24	369	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
27	359	CDD	cd06342	PBP1_ABC_LIVBP-like
16	23	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
26	363	Pfam	PF13458	Periplasmic binding protein
26	363	InterPro	IPR028081	Leucine-binding protein domain
7	15	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
144	272	Gene3D	G3DSA:3.40.50.2300	-
26	42	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
26	42	InterPro	IPR000709	Leu/Ile/Val-binding protein
254	272	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
254	272	InterPro	IPR000709	Leu/Ile/Val-binding protein
329	344	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
329	344	InterPro	IPR000709	Leu/Ile/Val-binding protein
67	85	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
67	85	InterPro	IPR000709	Leu/Ile/Val-binding protein
48	64	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
48	64	InterPro	IPR000709	Leu/Ile/Val-binding protein
277	290	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
277	290	InterPro	IPR000709	Leu/Ile/Val-binding protein
88	98	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
88	98	InterPro	IPR000709	Leu/Ile/Val-binding protein

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...

Legend High Medium Low

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_A0A0H3GZM8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_09592	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
4				0.385
16				0.316

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				1.65	0.027
2				1.08	0.007

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				1.26	0.012
2				1.18	0.01

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
ABU	3IP9	Q7CX36	103.1 Da LogP -0.19 TPSA 63.3	✓ Ro5	✓ Clean	`C(CC(=O)O)CN`

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
ZINC13357569	0.778	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCC(=O)O`
ZINC1763117	0.778	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCC(=O)O`
ZINC1845814	0.778	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCC(=O)O`
ZINC22048354	0.778	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCC(=O)O`
ZINC34552398	0.778	257.4 Da LogP 4.10 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCC(=O)O`
ZINC34628306	0.778	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCCC(=O)O`
ZINC3074822	0.667	229.3 Da LogP 2.11 TPSA 80.4	✓ Ro5	✓ Clean	`NCCCCCC(=O)CCCCCC(=O)O`
ZINC4822737	0.667	313.5 Da LogP 4.45 TPSA 80.4	✓ Ro5	✓ Clean	`NCCCCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC1569727	0.593	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](C)C(=O)O`
ZINC1569728	0.593	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@@H](C)C(=O)O`
ZINC1569729	0.593	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](C)C(=O)O`
ZINC1569730	0.593	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@H](C)C(=O)O`
ZINC1529497	0.588	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045	0.588	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115	0.588	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020	0.588	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440	0.588	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298	0.588	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062	0.588	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC2522597	0.586	246.3 Da LogP -0.60 TPSA 129.7	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)C[C@H](N)C(=O)O)C(=O)O`
ZINC40470158	0.577	216.3 Da LogP 0.49 TPSA 92.4	✓ Ro5	✓ Clean	`NCCCC(=O)NCCCCCC(=O)O`
ZINC1532219	0.571	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](CC(C)C)C(=O)O`
ZINC1532220	0.571	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@H](N)CC(C)C)C(=O)O`
ZINC1532221	0.571	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](CC(C)C)C(=O)O`
ZINC1532222	0.571	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@H](CC(C)C)C(=O)O`
ZINC64219359	0.565	202.3 Da LogP -0.41 TPSA 106.4	✓ Ro5	✓ Clean	`CC(C)[C@H](C(=O)[C@@H](C)N)[C@H](N)C(=O)O`
ZINC64219360	0.565	202.3 Da LogP -0.41 TPSA 106.4	✓ Ro5	✓ Clean	`CC(C)[C@@H](C(=O)[C@@H](C)N)[C@H](N)C(=O)O`
ZINC78311249	0.565	203.3 Da LogP -0.54 TPSA 92.6	✓ Ro5	✓ Clean	`NCCCN(CCCN)CCC(=O)O`
ZINC79670384	0.565	202.3 Da LogP -0.41 TPSA 106.4	✓ Ro5	✓ Clean	`CC(C)[C@@H](C(=O)[C@H](C)N)[C@H](N)C(=O)O`
ZINC79670387	0.565	202.3 Da LogP -0.41 TPSA 106.4	✓ Ro5	✓ Clean	`CC(C)[C@H](C(=O)[C@H](C)N)[C@H](N)C(=O)O`
ZINC1605717	0.552	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](C(=O)O)C(C)C`
ZINC1605718	0.552	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@H](C(=O)O)C(C)C`
ZINC1605719	0.552	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](C(=O)O)C(C)C`
ZINC1605720	0.552	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@@H](C(=O)O)C(C)C`
ZINC13433578	0.550	201.3 Da LogP 1.68 TPSA 80.4	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCC(=O)O`
ZINC201768036	0.542	279.3 Da LogP -0.12 TPSA 100.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCCC(=O)O`
ZINC1616450	0.536	254.3 Da LogP -1.28 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)[C@@H]1CCCN1)[C@@H]1CCCN1`
ZINC5600257	0.536	254.3 Da LogP -1.28 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)[C@H]1CCCN1)[C@H]1CCCN1`
ZINC8655607	0.536	254.3 Da LogP -1.28 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)[C@H]1CCCN1)[C@@H]1CCCN1`
ZINC13529436	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N1CCCCCC1`
ZINC1541834	0.533	218.3 Da LogP -1.08 TPSA 112.7	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](CO)C(=O)O`
ZINC19502834	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)N1CCCCCC1`
ZINC19502836	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](N)C(=O)N1CCCCCC1`
ZINC19502838	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](N)C(=O)N1CCCCCC1`
ZINC227596999	0.533	357.5 Da LogP 1.51 TPSA 121.5	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](CC(C)C)C(=O)N[C@H](CC…`
ZINC227597004	0.533	357.5 Da LogP 1.51 TPSA 121.5	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](CC(C)C)C(=O)N[C@H](C…`
ZINC2556618	0.533	246.3 Da LogP -0.60 TPSA 129.7	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC4556667	0.533	357.5 Da LogP 1.51 TPSA 121.5	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](CC(C)C)C(=O)N[C@@H](C…`
ZINC4556684	0.533	218.3 Da LogP -1.08 TPSA 112.7	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@@H](CO)C(=O)O`
ZINC4556685	0.533	218.3 Da LogP -1.08 TPSA 112.7	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@H](CO)C(=O)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.