KpKP13 Protein target profile

Alpha-amylase

Accession: KP13_00232

Gene: AHE42145.1 malS 3D evidence: Experimental + ColabFold model UniProt Q9RHR1

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Length 677

Pocket druggability (P2Rank · Experimental) 0.958

Direct ligand evidence 0 12 total records

Functional annotation 1 EC 7 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: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.96, FPocket 0.85). Use the 3D pocket comparison to verify whether they identify the same site. Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.85. 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: Hit
Human identity (%): 27.957 Lower values reduce human off-target concern.
Human E-value: 8.8e-06
Gut microbiome similarity: 1.7% 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.

Structure confidence

ColabFold pLDDT: 92.4 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.958

Structure 9US3

Pocket Pocket 1

Druggability (FPocket) 0.846

Structure 9US4

Pocket Pocket 1

ColabFold model

P2Rank 0.945 · Pocket 1

FPocket 0.598 · Pocket 27

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 82 / 4744 genomes with a hit

Prevalence 1.7%

Sequence

Primary amino-acid sequence viewer.

MKLAALATLFVPGMAFAAWTTTDFPAFTEEGTGRFISQKVVEKGTRPLQLNFDQQCWQPSGGIKLNQMLSMEPCRGTPPQWRIFRQGLYTLEVDTRSGTPTMMISLEEKETSAAAPQIRQCPKWDGKPLTIDVSKTFAEGSKVRDFYSGNVATVSGGKITLQPAFGSNGLLLLERAETAAPAPFDWHNATVYFVLTDRFVNGNPANDNSYGRHKDGMQEIGTFHGGDLQGLTSKLDYLQQMGVNALWISSPLEQIHGWVGGGTKGDFPHYAYHGYYTQDWSKLDANMGTEADLRRLVDEAHKRGIRILFDVVMNHAGYATLADMQEFQFGSLYLQGDELKKTLGERWTDWKPGAGQTWHSFNDYINFSDKAGWEKWWGKKWIRTDIGDYDNPGYDDLTMSLAFLPDLKTESKEISGLPNFYSHKPDTAAKAIPGYTPRDYLTHWLSQWVRDYGIDGFRVDTAKHVEMDAWQQLKTQATAALAEWKKANPDKALDAAPFWMTGEAWGHGVMQSDYYRHGFDAMINFDYQDQAAKAATCMANIDLTWQQMADKLQSFNVLSYLSSHDTRLFREGGTTAAELLLLAPGAVQIFYGDESSRPFGPTGSDPLQGTRSEMNWQDVNGKAARSVTHWQKIGQFRARHPAIGMGKQTTLSMSRGYGFVRESGEDKVMVIWAGQQQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization: Periplasmic

Enzyme Commission (EC)

3.2.1.98

Gene Ontology (GO)

GO:0030980 The chemical reactions and pathways resulting in the breakdown of alpha-glucans.
GO:0009313 The chemical reactions and pathways resulting in the breakdown of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
GO:0005509 Binding to a calcium ion (Ca2+).
GO:0004556 Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units.
GO:0033927 Catalysis of the hydrolysis of (1->4)-alpha-D-glucosidic linkages in amylaceous polysaccharides, to remove successive maltohexaose residues from the non-reducing chain ends.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

22 records

Show feature table

Start	End	DB	Term	Name
1	676	PIRSF	PIRSF036917	Alph_amls_MalS
1	676	InterPro	IPR014635	Alpha-amylase, MalS type
435	644	Gene3D	G3DSA:3.20.20.80	Glycosidases
176	416	Gene3D	G3DSA:3.20.20.80	Glycosidases
1	2	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
176	415	FunFam	G3DSA:3.20.20.80:FF:000089	Periplasmic alpha-amylase
1	17	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
176	672	PANTHER	PTHR10357	ALPHA-AMYLASE FAMILY MEMBER
429	642	FunFam	G3DSA:3.20.20.80:FF:000079	Alpha-amylase
1	17	SignalP_EUK	SignalP-noTM	SignalP-noTM
226	369	Pfam	PF00128	Alpha amylase, catalytic domain
226	369	InterPro	IPR006047	Glycosyl hydrolase, family 13, catalytic domain
440	594	Pfam	PF00128	Alpha amylase, catalytic domain
440	594	InterPro	IPR006047	Glycosyl hydrolase, family 13, catalytic domain
18	677	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
12	17	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
179	646	SUPERFAMILY	SSF51445	(Trans)glycosidases
179	646	InterPro	IPR017853	Glycoside hydrolase superfamily
3	11	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
193	637	SMART	SM00642	aamy
193	637	InterPro	IPR006047	Glycosyl hydrolase, family 13, catalytic domain
1	17	Phobius	SIGNAL_PEPTIDE	Signal peptide region

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

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.958

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Surrounding area

Pocket 2 P2Rank #2

0.441

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Surrounding area

Pocket 3 P2Rank #3

0.15

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Surrounding area

Pocket 4 P2Rank #4

0.096

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Surrounding area

Pocket 5 P2Rank #5

0.037

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Surrounding area

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.945

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Surrounding area

Pocket 2 P2Rank #2

0.295

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Surrounding area

Pocket 3 P2Rank #3

0.29

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Surrounding area

Pocket 4 P2Rank #4

0.232

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Surrounding area

Pocket 5 P2Rank #5

0.09

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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #27

0.598

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Surrounding area

Pocket 2 FPocket #20

0.336

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Surrounding area

All structural evidence 4 experimental · 1 predicted

Structural evidence

4 + 1

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
PDB 9US3	X-ray	1.90 Å	A,B	97.5% 18-677	PDBe RCSB PDBj File	Viewing
PDB 9US4	X-ray	1.95 Å	A,B	97.5% 18-677	PDBe RCSB PDBj File	Loaded
PDB 9US6	X-ray	2.70 Å	A,B	97.5% 18-677	PDBe RCSB PDBj File	Loaded
PDB 9US5	X-ray	2.66 Å	A	82.4% 120-677	PDBe RCSB PDBj File	Loaded
ColabFold KP13_00232	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.

12 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 5 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 7 similarity-based ZINC candidates

Best available ligand signal

ABC PDB via homolog 937.9 Da · LogP -10.86 · TPSA 439.0 Open detail RCSB PDB

ACI PDB via homolog Detail RCSB PDB

ARE PDB via homolog Detail RCSB PDB

FLC PDB via homolog Detail RCSB PDB

NOJ 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
ABC RCSB PDB	7TAA	P0C1B3	937.9 Da LogP -10.86 TPSA 439.0	3 viol.	✓ Clean	`C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@…`
ACI RCSB PDB	2CXG	P43379	175.2 Da LogP -2.67 TPSA 106.9	✓ Ro5	✓ Clean	`C1=C([C@H]([C@@H]([C@H]([C@H]1N)O)O)O)CO`
ARE RCSB PDB	3A6O	Q08751	807.7 Da LogP -10.74 TPSA 400.3	3 viol.	✓ Clean	`C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@…`
FLC RCSB PDB	6WNI	U5CJP3	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
NOJ RCSB PDB	1I75	P05618	163.2 Da LogP -2.97 TPSA 93.0	✓ Ro5	✓ Clean	`C1[C@@H]([C@H]([C@@H]([C@H](N1)CO)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
ZINC100055151 ZINC	0.500	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@H](O[C@H]2[C@H](O[C@@H]3[C@@H](CO)O…`
ZINC100055153 ZINC	0.500	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@H](O[C@H]2[C@H](O[C@@H]3[C@@H](CO)O…`
ZINC100055156 ZINC	0.500	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](CO)O[C@@H…`
ZINC100055157 ZINC	0.500	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](CO)O[C@@H…`
ZINC16123955 ZINC	0.500	204.2 Da LogP -2.82 TPSA 101.8	✓ Ro5	✓ Clean	`CC(=O)NC[C@H]1NC[C@H](O)[C@@H](O)[C@@H]1O`
ZINC2362797719 ZINC	0.500	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@@H](O[C@H]2[C@H](O[C@H]3[C@@H](O)[C…`
ZINC55537584 ZINC	0.500	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@@H](O[C@H]2[C@H](O[C@@H]3[C@@H](CO)…`

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.

Cross-references

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

Sequence

UniProt Q9RHR1

Structure

PDB 9US3 PDB 9US4 PDB 9US6 PDB 9US5