Protein profile

KP13_00522

ABC transporter arginine-binding protein 1

Genome: KpKP13

Gene: artJ AHE46744.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GH82

Export view

Amino acids 243

Annotations 3

Features 19

PDB binders 1

Druggability 0.837

Overview

Basic information about this protein and its source genome.

Accession: KP13_00522
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: artJ AHE46744.1
Status: annotated
Amino acids: 243
Structure source: AlphaFold + ColabFold

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0015276 Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts. 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: Periplasmic
ColabFold pLDDT: 93.09

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 0.837

Structure A0A0H3GH82

Pocket Pocket 1

P2Rank 0.422

Structure A0A0H3GH82

Pocket Pocket 1

ColabFold model

FPocket 0.793 · Pocket 1

P2Rank 0.349 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 12 / 4744 genomes with a hit

Normalized 0.003

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0015276 Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.
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.

19 records

Show feature table

Start	End	DB	Term	Name
16	20	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
6	242	PANTHER	PTHR35936	MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
1	242	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
1	20	Phobius	SIGNAL_PEPTIDE	Signal peptide region
109	202	Gene3D	G3DSA:3.40.190.10	-
22	243	SMART	SM00062	AABind_6
22	243	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
24	243	SMART	SM00079	GluR_14
24	243	InterPro	IPR001320	Ionotropic glutamate receptor, C-terminal
23	243	Pfam	PF00497	Bacterial extracellular solute-binding proteins, family 3
23	243	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	20	SignalP_EUK	SignalP-noTM	SignalP-noTM
1	20	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
25	241	Gene3D	G3DSA:3.40.190.10	-
21	243	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4	15	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
45	58	ProSitePatterns	PS01039	Bacterial extracellular solute-binding proteins, family 3 signature.
45	58	InterPro	IPR018313	Solute-binding protein family 3, conserved site

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_A0A0H3GH82	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00522	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				0.837

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				5.2	0.241
2				1.39	0.017

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				0.793

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	3.77	0.145
2	1.91	0.038
3	1.61	0.026

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
ORN	1LAH	P02911	132.2 Da LogP -0.86 TPSA 89.3	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)N)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
ZINC27644247	0.618	230.3 Da LogP 0.09 TPSA 111.2	✓ Ro5	✓ Clean	`CCCCNC(=N)NCCC[C@H](N)C(=O)O`
ZINC196899382	0.588	228.2 Da LogP -0.14 TPSA 92.4	✓ Ro5	✓ Clean	`N[C@@H](CCCNC(=O)C(F)(F)F)C(=O)O`
ZINC4155291	0.583	216.2 Da LogP -1.37 TPSA 130.8	✓ Ro5	✓ Clean	`CC(=O)/N=C(\N)NCCC[C@H](N)C(=O)O`
ZINC4155299	0.583	216.2 Da LogP -1.37 TPSA 130.8	✓ Ro5	✓ Clean	`CC(=O)/N=C(\N)NCCC[C@@H](N)C(=O)O`
ZINC1529718	0.571	202.3 Da LogP -0.74 TPSA 102.4	✓ Ro5	✓ Clean	`CN(C)C(=N)NCCC[C@H](N)C(=O)O`
ZINC1546170	0.571	216.3 Da LogP -0.30 TPSA 111.2	✓ Ro5	✓ Clean	`CCCNC(=N)NCCC[C@H](N)C(=O)O`
ZINC2560273	0.571	202.3 Da LogP -0.69 TPSA 111.2	✓ Ro5	✓ Clean	`CCNC(=N)NCCC[C@H](N)C(=O)O`
ZINC4543782	0.571	202.3 Da LogP -0.74 TPSA 102.4	✓ Ro5	✓ Clean	`CN(C)C(=N)NCCC[C@@H](N)C(=O)O`
ZINC7997269	0.571	205.3 Da LogP 0.07 TPSA 99.2	✓ Ro5	✓ Clean	`CSC(=N)NCCC[C@@H](N)C(=O)O`
ZINC144076260	0.559	232.2 Da LogP -0.84 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)CC(=O)O)C(=O)O`
ZINC218922593	0.559	204.2 Da LogP -1.32 TPSA 112.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)CO)C(=O)O`
ZINC2516116	0.559	275.3 Da LogP -1.12 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC4545887	0.559	275.3 Da LogP -1.12 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC4545888	0.559	275.3 Da LogP -1.12 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)NCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC4545889	0.559	275.3 Da LogP -1.12 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@H](CCCCNC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC50027904	0.559	261.3 Da LogP -1.51 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)C[C@H](N)C(=O)O)C(=O)O`
ZINC12503853	0.556	201.3 Da LogP 0.55 TPSA 99.2	✓ Ro5	✓ Clean	`CCCC(=N)NCCC[C@H](N)C(=O)O`
ZINC1640080	0.556	232.3 Da LogP 0.70 TPSA 101.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)NCCC[C@H](N)C(=O)O`
ZINC217503161	0.556	230.3 Da LogP 0.88 TPSA 92.4	✓ Ro5	✓ Clean	`CCCCC(=O)NCCCC[C@H](N)C(=O)O`
ZINC2560765	0.556	232.3 Da LogP 0.70 TPSA 101.6	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)NCCC[C@@H](N)C(=O)O`
ZINC3055005	0.556	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007	0.556	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010	0.556	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC675038108	0.556	231.3 Da LogP -1.49 TPSA 123.3	1 viol.	✓ Clean	`CNC(NC)C(=N)NCCC[C@H](N)C(=O)O`
ZINC100017163	0.553	213.3 Da LogP 0.71 TPSA 99.2	✓ Ro5	✓ Clean	`C/C=C/CC(=N)NCCC[C@H](N)C(=O)O`
ZINC19796052	0.553	219.2 Da LogP -1.73 TPSA 156.9	✓ Ro5	✓ Clean	`N/C(=N\[N+](=O)[O-])NCCC[C@H](N)C(=O)O`
ZINC21982226	0.553	219.2 Da LogP -1.73 TPSA 156.9	✓ Ro5	✓ Clean	`N/C(=N\[N+](=O)[O-])NCCC[C@@H](N)C(=O)O`
ZINC5113209	0.548	275.3 Da LogP -0.26 TPSA 138.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC13545298	0.543	202.3 Da LogP 0.09 TPSA 92.4	✓ Ro5	✓ Clean	`CCC(=O)NCCCC[C@H](N)C(=O)O`
ZINC216616240	0.543	430.5 Da LogP 0.72 TPSA 184.8	1 viol.	✓ Clean	`N[C@@H](CCCCNC(=O)CCCCCCC(=O)NCCCC[C@H](N)C(=O)…`
ZINC6360447	0.543	222.3 Da LogP 0.37 TPSA 75.3	✓ Ro5	✓ Clean	`N[C@H](CCCCNC(=S)S)C(=O)O`
ZINC1530092	0.541	254.2 Da LogP -1.61 TPSA 168.8	1 viol.	✓ Clean	`N=C(NCCC[C@H](N)C(=O)O)NP(=O)(O)O`
ZINC230402790	0.541	214.3 Da LogP 0.26 TPSA 92.4	✓ Ro5	✓ Clean	`C/C=C/C(=O)NCCCC[C@H](N)C(=O)O`
ZINC237993466	0.541	214.3 Da LogP 0.26 TPSA 92.4	✓ Ro5	✓ Clean	`C/C=C/C(=O)NCCCC[C@@H](N)C(=O)O`
ZINC2509855	0.541	216.2 Da LogP 0.09 TPSA 101.6	✓ Ro5	✓ Clean	`C=CCOC(=O)NCCC[C@H](N)C(=O)O`
ZINC5965908	0.541	202.3 Da LogP -1.03 TPSA 99.7	✓ Ro5	✓ Clean	`C/N=C(\NC)NCCC[C@H](N)C(=O)O`
ZINC98044182	0.541	216.2 Da LogP 0.09 TPSA 101.6	✓ Ro5	✓ Clean	`C=CCOC(=O)NCCC[C@@H](N)C(=O)O`
ZINC1555366	0.536	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1555367	0.536	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555369	0.536	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720127	0.536	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1720128	0.536	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720130	0.536	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1565131	0.528	200.2 Da LogP -0.13 TPSA 92.4	✓ Ro5	✓ Clean	`C=CC(=O)NCCCC[C@@H](N)C(=O)O`
ZINC1567145	0.528	218.3 Da LogP 0.31 TPSA 101.6	✓ Ro5	✓ Clean	`CCOC(=O)NCCCC[C@@H](N)C(=O)O`
ZINC1737889	0.528	245.3 Da LogP -0.33 TPSA 118.4	✓ Ro5	✓ Clean	`CC(C)[C@H](N)C(=O)NCCCC[C@H](N)C(=O)O`
ZINC1737892	0.528	245.3 Da LogP -0.33 TPSA 118.4	✓ Ro5	✓ Clean	`CC(C)[C@@H](N)C(=O)NCCCC[C@H](N)C(=O)O`
ZINC2041390	0.528	218.3 Da LogP 0.31 TPSA 101.6	✓ Ro5	✓ Clean	`CCOC(=O)NCCCC[C@H](N)C(=O)O`
ZINC2384794	0.528	242.2 Da LogP 0.25 TPSA 92.4	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)C(F)(F)F)C(=O)O`
ZINC6292525	0.528	242.2 Da LogP 0.25 TPSA 92.4	✓ Ro5	✓ Clean	`N[C@H](CCCCNC(=O)C(F)(F)F)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.