Protein target profile

KP13_05441

NAD(P)-binding domain-containing protein

Genome: KpKP13 Gene: AHE44968.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GS66

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Length 302

Pocket druggability 0.918

Direct ligand evidence 0 52 total records

Functional annotation 0 EC 2 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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

Main supporting evidence

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.92, P2Rank 0.98). Use the 3D pocket comparison to verify whether they identify the same site. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.92. This is a computational pocket signal, not binding validation. Review the complete evidence below

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: No hit
Gut microbiome similarity: 0.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 46.102 Higher values support similarity to known essential genes.
DEG E-value: 2.99e-68 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Unknown

Structure confidence

ColabFold pLDDT: 96.01 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 0.918

Structure A0A0H3GS66

Pocket Pocket 1

P2Rank 0.981

Structure A0A0H3GS66

Pocket Pocket 1

ColabFold model

FPocket 0.551 · Pocket 13

P2Rank 0.97 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 14 / 4744 genomes with a hit

Prevalence 0.3%

Cross-references

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

Sequence

UniProt A0A0H3GS66

Sequence

Primary amino-acid sequence viewer.

MMRIFLTGASGFIGSRILPALQASGHQVIGLARSESTAQALKAAGAEVHCGTLDAPESLLAGVGNADAVIHTAFDHDFSRFAANCEKDRQAILALGQALRGSTRPLVITSGTLMGDDGSGAPARESFFNSAHPSPRTASELAGQQLLEAGVDVRVVRLPQVHDTVRQGLLTCYIERAVANGAVALRGEGSNRWSAAHVDDVARLYVSALLQGAAGERYHAVAEEGIALRDIAAVIAHGLNLPLTHLDESQVDAWFGWFAPFTALDLRASSAWTRERLQWQPVGPGLLEDLQNMDYHKVTLSQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0004029 Catalysis of the reaction: an aldehyde + H2O + NAD+ = a carboxylate + 2 H+ + NADH.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
15	22	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
4	218	Pfam	PF01370	NAD dependent epimerase/dehydratase family
4	218	InterPro	IPR001509	NAD-dependent epimerase/dehydratase
2	293	PANTHER	PTHR48079	PROTEIN YEEZ
1	288	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
1	288	InterPro	IPR036291	NAD(P)-binding domain superfamily
4	14	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
23	302	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
2	290	CDD	cd05262	SDR_a7
1	22	Phobius	SIGNAL_PEPTIDE	Signal peptide region
3	283	Gene3D	G3DSA:3.40.50.720	-

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 · FPocket

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

Site 1 FPocket #1

0.918

Likely same site as P2Rank 1 2.5 Å 36 shared residues 92% of smaller site

Unusual size

Show in viewer

Surrounding area

Site 2 FPocket #18

0.373

Show in viewer

Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.981

Likely same site as FPocket 1 2.5 Å 36 shared residues 92% of smaller site

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_A0A0H3GS66	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_05441	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

UD1 PDB via homolog 607.4 Da · LogP -4.65 · TPSA 305.9 Open detail RCSB PDB

UD2 PDB via homolog Detail RCSB PDB

ZINC12959005 ZINC proposed compound · Tanimoto 0.632 Detail ZINC

ZINC12959016 ZINC proposed compound · Tanimoto 0.632 Detail ZINC

ZINC13548378 ZINC proposed compound · Tanimoto 0.632 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
UD1 RCSB PDB	6WJ9	Q4KCF6	607.4 Da LogP -4.65 TPSA 305.9	3 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O[P@@]…`
UD2 RCSB PDB	6WJA	Q4KCF6	607.4 Da LogP -4.65 TPSA 305.9	3 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1O[P@@](…`

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
ZINC12959005 ZINC	0.632	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)…`
ZINC12959016 ZINC	0.632	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@](=O)(O)O[P@](=O)(O…`
ZINC13548378 ZINC	0.632	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC25726233 ZINC	0.632	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@](=O)(O)O[P@](=O)(O)…`
ZINC3861755 ZINC	0.632	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875255 ZINC	0.632	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875256 ZINC	0.632	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)…`
ZINC3875257 ZINC	0.632	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875258 ZINC	0.632	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)…`
ZINC88466482 ZINC	0.632	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC35636069 ZINC	0.627	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)OP(=O)(O)O)[…`
ZINC40655887 ZINC	0.627	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)OP(=O)(O)O)[…`
ZINC40655889 ZINC	0.627	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC44460318 ZINC	0.627	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC4490939 ZINC	0.627	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC8585026 ZINC	0.627	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC8585028 ZINC	0.627	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O…`
ZINC8585030 ZINC	0.627	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC8585032 ZINC	0.627	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O…`
ZINC102211562 ZINC	0.611	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC110347779 ZINC	0.611	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC110347782 ZINC	0.611	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC97976147 ZINC	0.611	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC12503831 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC12503833 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC13512000 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC1532538 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC2026984 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC2123545 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC2606131 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC36377965 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC3870257 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC3870258 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@…`
ZINC3870259 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC3870260 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@…`
ZINC9235501 ZINC	0.567	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H…`
ZINC218568202 ZINC	0.560	498.2 Da LogP -1.85 TPSA 253.4	2 viol.	✓ Clean	`CO[C@H]1[C@@H](n2ccc(=O)[nH]c2=O)O[C@@H](CO[P@@…`
ZINC40576927 ZINC	0.560	498.2 Da LogP -1.85 TPSA 253.4	2 viol.	✓ Clean	`CO[C@@H]1[C@H](O)[C@@H](CO[P@@](=O)(O)O[P@@](=O…`
ZINC108477652 ZINC	0.554	486.1 Da LogP -1.52 TPSA 244.1	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)…`
ZINC145753022 ZINC	0.554	483.2 Da LogP -2.53 TPSA 270.2	2 viol.	✓ Clean	`N[C@@H]1[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC220143873 ZINC	0.554	486.1 Da LogP -1.52 TPSA 244.1	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC31519946 ZINC	0.554	486.1 Da LogP -1.52 TPSA 244.1	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)…`
ZINC78695900 ZINC	0.554	483.2 Da LogP -2.53 TPSA 270.2	2 viol.	✓ Clean	`N[C@@H]1[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC90614026 ZINC	0.554	486.1 Da LogP -1.52 TPSA 244.1	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC207686398 ZINC	0.534	438.2 Da LogP -1.91 TPSA 208.6	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)C(F)(F)P(=O)…`
ZINC11525576 ZINC	0.531	244.2 Da LogP -2.85 TPSA 124.8	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)c(=O)[…`
ZINC3834164 ZINC	0.531	244.2 Da LogP -2.85 TPSA 124.8	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c(=O…`
ZINC3870261 ZINC	0.531	244.2 Da LogP -2.85 TPSA 124.8	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c(=O)…`
ZINC6091549 ZINC	0.531	244.2 Da LogP -2.85 TPSA 124.8	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c(=O)[…`
ZINC7998085 ZINC	0.531	244.2 Da LogP -2.85 TPSA 124.8	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c(=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.