Protein target profile

KP13_02520

Lipoprotein nlpD

Genome: KpKP13 Gene: nlpD AHE42984.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWT3

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Length 378

Pocket druggability 0.005

Direct ligand evidence 0 22 total records

Functional annotation 0 EC 5 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.

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: 2.3% 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: OuterMembrane

Structure confidence

ColabFold pLDDT: 68.26 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 0.005

Structure A0A0H3GWT3

Pocket Pocket 10

P2Rank 0.301

Structure A0A0H3GWT3

Pocket Pocket 1

ColabFold model

FPocket 0.749 · Pocket 16

P2Rank 0.364 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 111 / 4744 genomes with a hit

Prevalence 2.3%

Cross-references

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

Sequence

UniProt A0A0H3GWT3

Sequence

Primary amino-acid sequence viewer.

MSAGSTKFTVSRIAALSLVSLWLAGCTNTNNPPAPVSSAGGAASSSTNSGMLITPPPSGVKSAPQAQPIQPMQTQTIQPQPAPVAQEPVQTVNGRIVYNRKYGDIPKGSYTGGSTYTVKRGDTLFYIAWVTGNDFRDLAQRNNIPAPYALNVGQVLQVGNASGQPITGENAVSQASARASGGATTSTTSAQKSTAVVASQPTITYSESSGEQSATKMLPNNKPATTTTTVVAPVTAPTTVSTTQPTASSTSTSSPISAWRWPTDGKVIENFSGAEGGNKGIDIAGSKGQAIVATADGRVVYAGNALRGYGNLIIIKHNDDYLSAYAHNDTMLVREQQEVKAGQKIATMGSTGTSSTRLHFEIRYKGKSVNPLQYLPQR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0032153 The eventual plane of cell division (also known as cell cleavage or cytokinesis) in a dividing cell. In Eukaryotes, the cleavage apparatus, composed of septin structures and the actomyosin contractile ring, forms along this plane, and the mitotic, or meiotic, spindle is aligned perpendicular to the division plane. In bacteria, the cell division site is generally located at mid-cell and is the site at which the cytoskeletal structure, the Z-ring, assembles.
GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

33 records

Show feature table

Start	End	DB	Term	Name
1	12	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
167	187	MobiDBLite	mobidb-lite	consensus disorder prediction
213	376	FunFam	G3DSA:2.70.70.10:FF:000004	NlpD family lipoprotein
108	166	FunFam	G3DSA:3.10.350.10:FF:000008	Murein hydrolase activator NlpD
114	157	Gene3D	G3DSA:3.10.350.10	LysM domain
114	157	InterPro	IPR036779	LysM domain superfamily
115	158	CDD	cd00118	LysM
115	158	InterPro	IPR018392	LysM domain
116	158	Pfam	PF01476	LysM domain
116	158	InterPro	IPR018392	LysM domain
39	378	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
278	371	Pfam	PF01551	Peptidase family M23
278	371	InterPro	IPR016047	Peptidase M23
115	375	SUPERFAMILY	SSF51261	Duplicated hybrid motif
115	375	InterPro	IPR011055	Duplicated hybrid motif
1	29	SignalP_EUK	SignalP-noTM	SignalP-noTM
115	159	SMART	SM00257	LysM_2
115	159	InterPro	IPR018392	LysM domain
13	26	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	38	Phobius	SIGNAL_PEPTIDE	Signal peptide region
35	86	MobiDBLite	mobidb-lite	consensus disorder prediction
1	26	ProSiteProfiles	PS51257	Prokaryotic membrane lipoprotein lipid attachment site profile.
278	362	CDD	cd12797	M23_peptidase
107	375	PANTHER	PTHR21666	PEPTIDASE-RELATED
219	376	Gene3D	G3DSA:2.70.70.10	Glucose Permease (Domain IIA)
219	376	InterPro	IPR011055	Duplicated hybrid motif
1	25	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
114	158	ProSiteProfiles	PS51782	LysM domain profile.
114	158	InterPro	IPR018392	LysM domain
27	38	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
63	86	MobiDBLite	mobidb-lite	consensus disorder prediction
35	55	MobiDBLite	mobidb-lite	consensus disorder prediction
1	24	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM

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

0.301

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Surrounding area

Site 2 P2Rank #2

0.214

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Surrounding area

Site 3 P2Rank #3

0.044

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Surrounding area

Site 4 P2Rank #4

0.017

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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

0.364

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Surrounding area

Site 2 P2Rank #2

0.361

Likely same site as FPocket 16 6.3 Å 7 shared residues 88% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.007

Likely same site as FPocket 16 4.6 Å 3 shared residues 75% of smaller site

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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_A0A0H3GWT3	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_02520	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.

22 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 3 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 19 similarity-based ZINC candidates

Best available ligand signal

4SQ PDB via homolog 281.2 Da · LogP -2.12 · TPSA 158.8 Open detail RCSB PDB

CAC PDB via homolog Detail RCSB PDB

TLA PDB via homolog Detail RCSB PDB

ZINC12359024 ZINC proposed compound · Tanimoto 0.692 Detail ZINC

ZINC13533920 ZINC proposed compound · Tanimoto 0.692 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
4SQ RCSB PDB	4ZYB	O33599	281.2 Da LogP -2.12 TPSA 158.8	✓ Ro5	✓ Clean	`C(CP(=O)(CNC(=O)CN)O)C(=O)NCC(=O)O`
CAC RCSB PDB	2B0P	O33599	137.0 Da LogP -0.52 TPSA 40.1	✓ Ro5	✓ Clean	`C[As](=O)(C)[O-]`
TLA RCSB PDB	2B13	O33599	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@@H]([C@H](C(=O)O)O)(C(=O)O)O`

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
ZINC12359024 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC13533920 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532740 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC2013424 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC3860635 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O`
ZINC5783661 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC6072527 ZINC	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1560405156 ZINC	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(\O)[C@H](O)[C@H](O)C(=O)O`
ZINC1560405157 ZINC	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(/O)[C@H](O)[C@H](O)C(=O)O`
ZINC2561009 ZINC	0.571	203.2 Da LogP -2.35 TPSA 121.5	✓ Ro5	✓ Clean	`NCC(=O)NCCC(=O)NCC(=O)O`
ZINC1569725 ZINC	0.545	246.2 Da LogP -3.62 TPSA 150.6	✓ Ro5	✓ Clean	`NCC(=O)NCC(=O)NCC(=O)NCC(=O)O`
ZINC4545903 ZINC	0.545	360.3 Da LogP -5.39 TPSA 208.8	1 viol.	✓ Clean	`NCC(=O)NCC(=O)NCC(=O)NCC(=O)NCC(=O)NCC(=O)O`
ZINC4545906 ZINC	0.545	303.3 Da LogP -4.51 TPSA 179.7	1 viol.	✓ Clean	`NCC(=O)NCC(=O)NCC(=O)NCC(=O)NCC(=O)O`
ZINC1529331 ZINC	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@H](C(=O)O)[C@@H](O)C(=O)O`
ZINC1529332 ZINC	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@H](C(=O)O)[C@H](O)C(=O)O`
ZINC1529333 ZINC	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@@H](C(=O)O)[C@@H](O)C(=O)O`
ZINC1529334 ZINC	0.500	206.1 Da LogP -2.21 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)[C@@H](C(=O)O)[C@H](O)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.

KP13_02520

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