Protein target profile

VK055_0026

bacterial extracellular solute-binding, 3 familyprotein

Genome: KpATCC43816 Gene: AIK78657.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GV06

Export view

Length 266

Pocket druggability 0.645

Direct ligand evidence 0 52 total records

Functional annotation 0 EC 4 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.65. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 2 structural and 0 bioactivity records.

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target: Hit
Human identity (%): 35.714 Lower values reduce human off-target concern.
Human E-value: 5.15e-06
Gut microbiome similarity: 2.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 38.655 Higher values support similarity to known essential genes.

Localization

Localization: Periplasmic

Structure confidence

ColabFold pLDDT: 89.6 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.645

Structure A0A0H3GV06

Pocket Pocket 3

P2Rank 0.423

Structure A0A0H3GV06

Pocket Pocket 1

ColabFold model

FPocket 0.737 · Pocket 5

P2Rank 0.539 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 97 / 4744 genomes with a hit

Prevalence 2.0%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GV06

Sequence

Primary amino-acid sequence viewer.

MKLALLGRQAMMGAMAVVLMAGVSVKTFAAENLLNQIKERGTLRVGLEGTYPPFSFQGDDGKLTGFEVEFANELAKHLGVKADLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTVSGVQALVKKGNEGVIKTAADLKGKKVGVGLGTNYEEWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKKTNNTLAVTGEAFSRQEAGVALRKGNDDLLKAVDGAIADMQKDGSLKALSEKWFGADVTK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 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.
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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
127	222	Gene3D	G3DSA:3.40.190.10	-
42	263	SMART	SM00062	AABind_6
42	263	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
13	24	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	29	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
42	262	SMART	SM00079	GluR_14
42	262	InterPro	IPR001320	Ionotropic glutamate receptor, C-terminal
127	222	FunFam	G3DSA:3.40.190.10:FF:000067	Cystine ABC transporter substrate-binding protein
11	264	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
65	78	ProSitePatterns	PS01039	Bacterial extracellular solute-binding proteins, family 3 signature.
65	78	InterPro	IPR018313	Solute-binding protein family 3, conserved site
1	12	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
42	261	CDD	cd13712	PBP2_FliY
30	266	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	29	Phobius	SIGNAL_PEPTIDE	Signal peptide region
43	261	Pfam	PF00497	Bacterial extracellular solute-binding proteins, family 3
43	261	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
45	260	Gene3D	G3DSA:3.40.190.10	-
25	29	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
15	264	PANTHER	PTHR35936	MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

Pocket score High Medium Low

How colors and pocket overlays are used

Uniform protein color marks the displayed model as a single molecular object.

Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.

Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.

'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.

'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.

'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #3

0.645

Show in viewer

Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.423

Show in viewer

Surrounding area

Site 2 P2Rank #2

0.016

Show in viewer

Surrounding area

Site 3 P2Rank #3

0.012

Show in viewer

Surrounding area

All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold DB AF_A0A0H3GV06	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_0026	ColabFold	—	—	full sequence	—	Loaded

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.

52 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 2 records from similar proteins

Structural ligands 2 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

ORN PDB via homolog 132.2 Da · LogP -0.86 · TPSA 89.3 Open detail RCSB PDB

SLZ PDB via homolog Detail RCSB PDB

ZINC2390999 ZINC proposed compound · Tanimoto 0.655 Detail ZINC

ZINC27644247 ZINC proposed compound · Tanimoto 0.618 Detail ZINC

ZINC196899382 ZINC proposed compound · Tanimoto 0.588 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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 RCSB PDB	3VVD	Q72JG5	132.2 Da LogP -0.86 TPSA 89.3	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)N)CN`
SLZ RCSB PDB	3VV5	Q72JG5	164.2 Da LogP -0.91 TPSA 89.3	✓ Ro5	✓ Clean	`C(CSC[C@@H](C(=O)O)N)N`

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
ZINC2390999 ZINC	0.655	275.3 Da LogP -1.99 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC27644247 ZINC	0.618	230.3 Da LogP 0.09 TPSA 111.2	✓ Ro5	✓ Clean	`CCCCNC(=N)NCCC[C@H](N)C(=O)O`
ZINC196899382 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	0.571	216.3 Da LogP -0.30 TPSA 111.2	✓ Ro5	✓ Clean	`CCCNC(=N)NCCC[C@H](N)C(=O)O`
ZINC2560273 ZINC	0.571	202.3 Da LogP -0.69 TPSA 111.2	✓ Ro5	✓ Clean	`CCNC(=N)NCCC[C@H](N)C(=O)O`
ZINC4543782 ZINC	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 ZINC	0.571	205.3 Da LogP 0.07 TPSA 99.2	✓ Ro5	✓ Clean	`CSC(=N)NCCC[C@@H](N)C(=O)O`
ZINC144076260 ZINC	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 ZINC	0.559	204.2 Da LogP -1.32 TPSA 112.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)CO)C(=O)O`
ZINC2516116 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	0.556	201.3 Da LogP 0.55 TPSA 99.2	✓ Ro5	✓ Clean	`CCCC(=N)NCCC[C@H](N)C(=O)O`
ZINC1640080 ZINC	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 ZINC	0.556	230.3 Da LogP 0.88 TPSA 92.4	✓ Ro5	✓ Clean	`CCCCC(=O)NCCCC[C@H](N)C(=O)O`
ZINC2560765 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	0.543	202.3 Da LogP 0.09 TPSA 92.4	✓ Ro5	✓ Clean	`CCC(=O)NCCCC[C@H](N)C(=O)O`
ZINC216616240 ZINC	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 ZINC	0.543	222.3 Da LogP 0.37 TPSA 75.3	✓ Ro5	✓ Clean	`N[C@H](CCCCNC(=S)S)C(=O)O`
ZINC1530092 ZINC	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 ZINC	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 ZINC	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 ZINC	0.541	216.2 Da LogP 0.09 TPSA 101.6	✓ Ro5	✓ Clean	`C=CCOC(=O)NCCC[C@H](N)C(=O)O`
ZINC5965908 ZINC	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 ZINC	0.541	216.2 Da LogP 0.09 TPSA 101.6	✓ Ro5	✓ Clean	`C=CCOC(=O)NCCC[C@@H](N)C(=O)O`
ZINC5131766 ZINC	0.538	224.3 Da LogP -1.26 TPSA 92.4	✓ Ro5	✓ Clean	`N[C@@H](CS)C(=O)N[C@@H](CS)C(=O)O`
ZINC1555366 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	0.528	200.2 Da LogP -0.13 TPSA 92.4	✓ Ro5	✓ Clean	`C=CC(=O)NCCCC[C@@H](N)C(=O)O`
ZINC1567145 ZINC	0.528	218.3 Da LogP 0.31 TPSA 101.6	✓ Ro5	✓ Clean	`CCOC(=O)NCCCC[C@@H](N)C(=O)O`
ZINC1737889 ZINC	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 ZINC	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`
ZINC1737894 ZINC	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`

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.