Protein target profile

KP13_04201

Phosphoserine aminotransferase

Genome: KpKP13 Gene: AHE45432.1 serC 3D evidence: Experimental + ColabFold model UniProt A6T700

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Length 362

Pocket druggability 0.699

Direct ligand evidence 0 42 total records

Functional annotation 0 EC 3 GO

Target summary

Promising target candidate with multiple supporting evidence streams.

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

Main supporting evidence

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. Moderate predicted binding pocket FPocket selected-pocket score 0.70. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.76. 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 (%): 47.814 Lower values reduce human off-target concern.
Human E-value: 1.14e-118
Gut microbiome similarity: 5.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 65.738 Higher values support similarity to known essential genes.
DEG E-value: 7.58e-172 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 98.03 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.699

Structure 7T7J

Pocket Pocket 3

P2Rank 0.763

Structure 7T7J

Pocket Pocket 1

ColabFold model

FPocket 0.845 · Pocket 1

P2Rank 0.462 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 252 / 4744 genomes with a hit

Prevalence 5.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MAQVYNFSSGPAMLPAEVLKLAQQELCDWHGLGTSVMEISHRGKEFIQVAEEAEQDFRALLNIPSNYKVLFCHGGGRGQFAGIPLNILGDKKVADYVDAGYWAASAVKEAKKYCTPNVIDAKITVDGKRAVKPMSEWQLTPGAAYLHYCPNETIDGIAIDETPNFGDDVIVTADFSSTILSREIDVNRFGVIYAGAQKNIGPAGLTLVIVREDLLGKASVACPSILDYTVLSENDSMFNTPPTFAWYLAGLVFKWLKQQGGVAAMDKINQQKAELLYGVIDNSGFYRNDVAQANRSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLDGVKALTDFMLDFERRHG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0006564 The chemical reactions and pathways resulting in the formation of L-serine.
GO:0004648 Catalysis of the reaction: O-phospho-L-serine + 2-oxoglutarate = 3-phosphonooxypyruvate + L-glutamate.

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	362	PIRSF	PIRSF000525	SerC
1	362	InterPro	IPR022278	Phosphoserine aminotransferase
16	258	FunFam	G3DSA:3.40.640.10:FF:000010	Phosphoserine aminotransferase
2	361	Hamap	MF_00160	Phosphoserine aminotransferase [serC].
2	361	InterPro	IPR022278	Phosphoserine aminotransferase
4	361	NCBIfam	TIGR01364	phosphoserine transaminase
4	361	InterPro	IPR022278	Phosphoserine aminotransferase
5	359	CDD	cd00611	PSAT_like
5	359	InterPro	IPR022278	Phosphoserine aminotransferase
189	208	ProSitePatterns	PS00595	Aminotransferases class-V pyridoxal-phosphate attachment site.
189	208	InterPro	IPR020578	Aminotransferase class-V, pyridoxal-phosphate binding site
3	362	SUPERFAMILY	SSF53383	PLP-dependent transferases
3	362	InterPro	IPR015424	Pyridoxal phosphate-dependent transferase
260	362	Gene3D	G3DSA:3.90.1150.10	Aspartate Aminotransferase, domain 1
260	362	InterPro	IPR015422	Pyridoxal phosphate-dependent transferase, small domain
16	259	Gene3D	G3DSA:3.40.640.10	-
16	259	InterPro	IPR015421	Pyridoxal phosphate-dependent transferase, major domain
2	361	PANTHER	PTHR43247	PHOSPHOSERINE AMINOTRANSFERASE
259	362	FunFam	G3DSA:3.90.1150.10:FF:000006	Phosphoserine aminotransferase
4	350	Pfam	PF00266	Aminotransferase class-V
4	350	InterPro	IPR000192	Aminotransferase class V domain

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 #3

0.699

Likely same site as P2Rank 2 3.0 Å 7 shared residues 78% of smaller site

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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

0.763

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Surrounding area

Site 2 P2Rank #2

0.115

Likely same site as FPocket 3 3.0 Å 7 shared residues 78% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.017

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Surrounding area

Site 4 P2Rank #4

0.002

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Surrounding area

Site 5 P2Rank #5

0.002

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Surrounding area

All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 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 7T7J	X-ray	—	A	—	PDBe RCSB PDBj File	Viewing
ColabFold KP13_04201	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.

42 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records

Transferred evidence 4 records from similar proteins

Structural ligands 3 0 loaded crystals

Measured bioactivity 1 direct and transferred ChEMBL records

Proposed compounds 38 similarity-based ZINC candidates

Best available ligand signal

GAM PDB via homolog 161.2 Da · LogP -0.35 · TPSA 100.6 Open detail RCSB PDB

PMP PDB via homolog Detail RCSB PDB

SEP PDB via homolog Detail RCSB PDB

DWT ChEMBL via homolog · pchembl 6.58 (~263.0 nM) Detail ChEMBL

ZINC1532708 ZINC proposed compound · Tanimoto 1.000 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
GAM RCSB PDB	1BJO	P23721	161.2 Da LogP -0.35 TPSA 100.6	✓ Ro5	✓ Clean	`C[C@](CCC(=O)O)(C(=O)O)N`
PMP RCSB PDB	6CZY	Q96255	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CN)O`
SEP RCSB PDB	4AZJ	Q9RME2	185.1 Da LogP -1.49 TPSA 130.1	✓ Ro5	✓ Clean	`C([C@@H](C(=O)O)N)OP(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DWT ChEMBL	Q9Y617	6.58 ~263.0 nM	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`

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
ZINC1532708 ZINC	1.000	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CN)c1O`
ZINC1532705 ZINC	0.769	249.2 Da LogP 0.20 TPSA 120.1	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CO)c1O`
ZINC1656021 ZINC	0.692	233.2 Da LogP 1.01 TPSA 99.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C)c1O`
ZINC1532514 ZINC	0.643	247.1 Da LogP 0.52 TPSA 117.0	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C=O)c1O`
ZINC197248777 ZINC	0.621	213.1 Da LogP -1.01 TPSA 119.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@H](N)COP(=O)(O)O`
ZINC197248785 ZINC	0.621	213.1 Da LogP -1.01 TPSA 119.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@@H](N)COP(=O)(O)O`
ZINC64219269 ZINC	0.615	203.2 Da LogP 0.68 TPSA 100.6	✓ Ro5	✓ Clean	`CC(C)(C)[C@](N)(CCC(=O)O)C(=O)O`
ZINC2139751 ZINC	0.600	253.2 Da LogP -0.08 TPSA 137.9	✓ Ro5	✓ Clean	`C[C@@](N)(CC[P@](=O)(O)CCC(=O)O)C(=O)O`
ZINC2139752 ZINC	0.600	253.2 Da LogP -0.08 TPSA 137.9	✓ Ro5	✓ Clean	`C[C@](N)(CC[P@](=O)(O)CCC(=O)O)C(=O)O`
ZINC1758357 ZINC	0.583	218.2 Da LogP 0.81 TPSA 111.9	✓ Ro5	✓ Clean	`CC(CCC(=O)O)(CCC(=O)O)C(=O)O`
ZINC1857358 ZINC	0.565	247.2 Da LogP 0.28 TPSA 137.9	✓ Ro5	✓ Clean	`NC(CCC(=O)O)(CCC(=O)O)CCC(=O)O`
ZINC3869233 ZINC	0.552	266.0 Da LogP -1.34 TPSA 170.8	✓ Ro5	✓ Clean	`O=C(O)[C@H](COP(=O)(O)O)OP(=O)(O)O`
ZINC3869234 ZINC	0.552	266.0 Da LogP -1.34 TPSA 170.8	✓ Ro5	✓ Clean	`O=C(O)[C@@H](COP(=O)(O)O)OP(=O)(O)O`
ZINC220133900 ZINC	0.538	398.3 Da LogP 3.77 TPSA 85.1	✓ Ro5	✓ Clean	`Cc1nc2nc(-c3cccnc3)nn2cc1C(=O)Nc1cccc(C(F)(F)F)…`
ZINC100300547 ZINC	0.536	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@](C)(N)C(=O)O`
ZINC1652265 ZINC	0.536	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@](C)(N)C(=O)O`
ZINC20148987 ZINC	0.532	414.4 Da LogP 4.50 TPSA 97.1	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1Nc1cncc(C(N)…`
ZINC1529994 ZINC	0.523	219.1 Da LogP -0.02 TPSA 118.6	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(N)n1`
ZINC2114966 ZINC	0.519	332.2 Da LogP 0.99 TPSA 149.5	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(/C=N/CCCC(=O)O)c1O`
ZINC4655041 ZINC	0.514	270.2 Da LogP -1.99 TPSA 181.0	1 viol.	✓ Clean	`N=C(N)NCCO[P@@](=O)(O)OC[C@H](N)C(=O)O`
ZINC9306398 ZINC	0.512	398.3 Da LogP 3.77 TPSA 85.1	✓ Ro5	✓ Clean	`Cc1c(C(=O)Nc2cccc(C(F)(F)F)c2)cnc2nc(-c3cccnc3)…`
ZINC13213450 ZINC	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@@H]2N[C@H](C(=O)O)CS2)c…`
ZINC13213453 ZINC	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@H]2N[C@H](C(=O)O)CS2)c1O`
ZINC13213455 ZINC	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@@H]2N[C@@H](C(=O)O)CS2)…`
ZINC13213457 ZINC	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@H]2N[C@@H](C(=O)O)CS2)c…`
ZINC5049572 ZINC	0.507	336.3 Da LogP 4.22 TPSA 58.2	✓ Ro5	✓ Clean	`CC(=O)Nc1cc(C(=O)Nc2cccc(C(F)(F)F)c2)ccc1C`
ZINC12501558 ZINC	0.500	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(…`
ZINC12501560 ZINC	0.500	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O…`
ZINC12501562 ZINC	0.500	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)…`
ZINC12501564 ZINC	0.500	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(…`
ZINC1532623 ZINC	0.500	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(…`
ZINC1586422 ZINC	0.500	216.2 Da LogP 1.31 TPSA 91.7	✓ Ro5	✓ Clean	`CC(=O)C(C)(CCC(=O)O)CCC(=O)O`
ZINC1712438 ZINC	0.500	248.2 Da LogP -0.13 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)CCC(CCC(=O)O)(C(=O)O)C(=O)O`
ZINC2047359 ZINC	0.500	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC2545091 ZINC	0.500	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O…`
ZINC3869602 ZINC	0.500	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC3869603 ZINC	0.500	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC3869604 ZINC	0.500	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=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.