Protein target profile

KP13_01017

Lysine-arginine-ornithine-binding periplasmic protein

Genome: KpKP13 Gene: argT AHE43455.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWD2

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Length 260

Pocket druggability 0.166

Direct ligand evidence 0 58 total records

Functional annotation 0 EC 3 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

Risks to review

Microbiome similarity 97 of 4744 screened genomes (2.0%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.17. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.03.

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: No hit
Gut microbiome similarity: 2.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Localization

Localization: Periplasmic

Structure confidence

ColabFold pLDDT: 93.52 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 0.166

Structure A0A0H3GWD2

Pocket Pocket 3

P2Rank 0.034

Structure A0A0H3GWD2

Pocket Pocket 1

ColabFold model

FPocket 0.254 · Pocket 7

P2Rank 0.058 · 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 A0A0H3GWD2

Sequence

Primary amino-acid sequence viewer.

MKKTILALSLLVGMSSTASVFAALPQSIRIGTDATYAPFSSKDAKGDFVGFDIDLGNELCSRIKVKCTWVGSDFDSLIPSLKAKKIDAIISSLSITEKRQQEIAFSDKLYAADSRLIAAKGSPIQPTLEALKGKHVGVLQGSTQEAYANDRWRSQGVDVVAYQNQDLIYSDLAAGRLDAALQDEVAASEGFLKQPAGKDFAFAGPSVKDKKYFGDGTGIGLRKDDAELKAAFDKALGEMRKDGTYDKMAKKYFDFNVYGD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0071705 The directed movement of nitrogen-containing compounds 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: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.

21 records

Show feature table

Start	End	DB	Term	Name
1	22	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
4	14	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
6	253	PANTHER	PTHR35936	MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
23	260	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	22	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
113	213	FunFam	G3DSA:3.40.190.10:FF:000020	Histidine ABC transporter substrate-binding periplasmic protein
50	63	ProSitePatterns	PS01039	Bacterial extracellular solute-binding proteins, family 3 signature.
50	63	InterPro	IPR018313	Solute-binding protein family 3, conserved site
26	257	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
15	22	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
113	213	Gene3D	G3DSA:3.40.190.10	-
27	256	SMART	SM00062	AABind_6
27	256	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
28	254	Pfam	PF00497	Bacterial extracellular solute-binding proteins, family 3
28	254	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
25	253	CDD	cd13703	PBP2_HisJ_LAO
1	22	Phobius	SIGNAL_PEPTIDE	Signal peptide region
4	253	NCBIfam	TIGR01096	lysine/arginine/ornithine ABC transporter substrate-binding protein
4	253	InterPro	IPR005768	Specific amino acids and opine-binding periplasmic protein, ABC transporter
29	252	Gene3D	G3DSA:3.40.190.10	-

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.

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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 · P2Rank

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

Site 1 P2Rank #1

0.034

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Surrounding area

Site 2 P2Rank #2

0.03

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Surrounding area

Site 3 P2Rank #3

0.028

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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.058

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Surrounding area

Site 2 P2Rank #2

0.032

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Surrounding area

Site 3 P2Rank #3

0.018

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Surrounding area

Site 4 P2Rank #4

0.006

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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_A0A0H3GWD2	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_01017	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.

58 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 8 records from similar proteins

Structural ligands 8 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

2W2 PDB via homolog 304.3 Da · LogP -1.39 · TPSA 185.8 Open detail RCSB PDB

6DB PDB via homolog Detail RCSB PDB

AOZ PDB via homolog Detail RCSB PDB

AQK PDB via homolog Detail RCSB PDB

AQQ PDB via homolog Detail RCSB PDB

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
2W2 RCSB PDB	5OVZ	P35120	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`[H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](CCC(=O)O)C…`
6DB RCSB PDB	5ITO	P35120	246.3 Da LogP -1.23 TPSA 148.5	1 viol.	✓ Clean	`[H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](C)C(=O)O`
AOZ RCSB PDB	5OT9	P35120	227.2 Da LogP -0.53 TPSA 115.3	✓ Ro5	✓ Clean	`CC(C(=O)O)NC(Cc1c[nH]cn1)C(=O)O`
AQK RCSB PDB	5OTC	P35120	190.2 Da LogP -1.15 TPSA 112.7	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)NCC(=O)O)CN`
AQQ RCSB PDB	5OTA	P35120	204.2 Da LogP -0.76 TPSA 112.6	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)N[C@@H](CCCN)C(=O)O`
OP1 RCSB PDB	4POW	P35120	286.3 Da LogP -1.22 TPSA 156.8	✓ Ro5	✓ Clean	`[H]/N=C(\N)/NCCC[C@@H](C(=O)O)N1[C@H](CCC1=O)C(…`
ORN RCSB PDB	1LAH	P02911	132.2 Da LogP -0.86 TPSA 89.3	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)N)CN`
TOE RCSB PDB	5ITO	P35120	164.2 Da LogP -0.34 TPSA 47.9	✓ Ro5	✓ Clean	`COCCOCCOCCO`

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
ZINC1580161 ZINC	1.000	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118 ZINC	1.000	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257 ZINC	1.000	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654 ZINC	1.000	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059 ZINC	1.000	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101 ZINC	1.000	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860 ZINC	1.000	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC575419714 ZINC	0.727	312.4 Da LogP 0.42 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCSCCOCCOCCO`
ZINC115163232 ZINC	0.700	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCCO`
ZINC258837490 ZINC	0.700	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCCO`
ZINC12501520 ZINC	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1692489 ZINC	0.688	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC3874716 ZINC	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769 ZINC	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548 ZINC	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC4530388 ZINC	0.688	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5178829 ZINC	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830 ZINC	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5701172 ZINC	0.688	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC5997861 ZINC	0.688	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC575432150 ZINC	0.667	344.4 Da LogP -0.89 TPSA 100.5	✓ Ro5	✓ Clean	`COCCOCCOCCS(=O)(=O)CCOCCOCCO`
ZINC19815880 ZINC	0.659	213.2 Da LogP -0.24 TPSA 104.3	✓ Ro5	✓ Clean	`COC(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O`
ZINC1857524240 ZINC	0.652	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`COCCNCCOCCOCCO`
ZINC22148708 ZINC	0.651	239.3 Da LogP 0.57 TPSA 95.1	✓ Ro5	✓ Clean	`CC(C)CC(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O`
ZINC22148712 ZINC	0.651	239.3 Da LogP 0.57 TPSA 95.1	✓ Ro5	✓ Clean	`CC(C)CC(=O)N[C@H](Cc1c[nH]cn1)C(=O)O`
ZINC1570743 ZINC	0.628	239.3 Da LogP 0.57 TPSA 95.1	✓ Ro5	✓ Clean	`CC(C)(C)C(=O)N[C@H](Cc1c[nH]cn1)C(=O)O`
ZINC4899806 ZINC	0.622	254.3 Da LogP -0.50 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)[C@H](N)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O`
ZINC31393708 ZINC	0.619	235.1 Da LogP -0.91 TPSA 135.5	✓ Ro5	✓ Clean	`O=C(O)[C@H](Cc1c[nH]cn1)NP(=O)(O)O`
ZINC1570742 ZINC	0.614	223.2 Da LogP 0.10 TPSA 95.1	✓ Ro5	✓ Clean	`C=C(C)C(=O)N[C@H](Cc1c[nH]cn1)C(=O)O`
ZINC5500513 ZINC	0.614	223.2 Da LogP 0.10 TPSA 95.1	✓ Ro5	✓ Clean	`C=C(C)C(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O`
ZINC13600073 ZINC	0.605	229.3 Da LogP -0.55 TPSA 95.1	✓ Ro5	✓ Clean	`O=C(CS)N[C@@H](Cc1c[nH]cn1)C(=O)O`
ZINC5650743 ZINC	0.600	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917 ZINC	0.600	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
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`
ZINC257666436 ZINC	0.587	261.3 Da LogP 0.92 TPSA 103.8	✓ Ro5	✓ Clean	`Cc1cc(C)nc(N[C@@H](Cc2c[nH]cn2)C(=O)O)n1`
ZINC116078641 ZINC	0.583	222.2 Da LogP -0.80 TPSA 74.2	✓ Ro5	✓ Clean	`COC(=O)COCCOCCOCCO`
ZINC1857790631 ZINC	0.583	280.3 Da LogP -0.39 TPSA 83.5	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCOCCO`
ZINC196151418 ZINC	0.583	266.3 Da LogP -0.78 TPSA 83.5	✓ Ro5	✓ Clean	`COC(=O)COCCOCCOCCOCCO`
ZINC202958272 ZINC	0.583	236.3 Da LogP -0.41 TPSA 74.2	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCO`
ZINC20567519 ZINC	0.583	321.3 Da LogP -1.07 TPSA 135.7	✓ Ro5	Alert	`CN1C(=O)C(=CN[C@@H](Cc2c[nH]cn2)C(=O)O)C(=O)N(C…`
ZINC20567520 ZINC	0.583	321.3 Da LogP -1.07 TPSA 135.7	✓ Ro5	Alert	`CN1C(=O)C(=CN[C@H](Cc2c[nH]cn2)C(=O)O)C(=O)N(C)…`
ZINC34111591 ZINC	0.583	207.3 Da LogP -1.06 TPSA 62.2	✓ Ro5	✓ Clean	`COCCOCCN(CCO)CCO`
ZINC642881862 ZINC	0.583	324.4 Da LogP -0.38 TPSA 92.7	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCOCCOCCO`
ZINC1568163 ZINC	0.578	259.3 Da LogP 0.84 TPSA 95.1	✓ Ro5	✓ Clean	`O=C(N[C@H](Cc1c[nH]cn1)C(=O)O)c1ccccc1`
ZINC15919758 ZINC	0.578	245.3 Da LogP 1.20 TPSA 78.0	✓ Ro5	✓ Clean	`O=C(O)[C@H](Cc1c[nH]cn1)NCc1ccccc1`
ZINC8583964 ZINC	0.578	226.2 Da LogP -1.13 TPSA 121.1	✓ Ro5	✓ Clean	`NCCC(=O)N[C@H](Cc1c[nH]cn1)C(=O)O`
ZINC218761131 ZINC	0.574	261.3 Da LogP 0.29 TPSA 103.8	✓ Ro5	✓ Clean	`Cc1ncc(CN[C@@H](Cc2c[nH]cn2)C(=O)O)cn1`
ZINC218761171 ZINC	0.574	261.3 Da LogP 0.29 TPSA 103.8	✓ Ro5	✓ Clean	`Cc1ncc(CN[C@H](Cc2c[nH]cn2)C(=O)O)cn1`
ZINC2525827 ZINC	0.563	268.3 Da LogP -0.95 TPSA 124.2	✓ Ro5	✓ Clean	`CC(=O)NCCC(=O)N[C@@H](Cc1c[nH]cn1)C(=O)O`
ZINC218760743 ZINC	0.560	304.4 Da LogP 0.81 TPSA 115.8	✓ Ro5	✓ Clean	`CC(C)Nc1ncc(CN[C@H](Cc2c[nH]cn2)C(=O)O)cn1`

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.

KP13_01017

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

Main supporting evidence

Risks to review

Evidence gaps

Prioritization evidence

Off-target risk

Essentiality

Localization

Structure confidence

Binding-site evidence

Cross-references

Sequence

Sequence

Functional annotations

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · P2Rank

Binding pockets · FPocket

Binding pockets · P2Rank

Structural evidence

Ligand evidence