KpATCC43816 Protein target profile

phosphoserine phosphatase SerB

Accession: VK055_2588

Gene: AIK81185.1 serB 3D evidence: AlphaFold DB model + ColabFold model Metabolism 3 reactions UniProt A0A0H3GRD6

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Length 323

Pocket druggability (P2Rank · AlphaFold DB model) 0.849

Metabolic reactions 3

Chokepoint No

Direct ligand evidence 0 57 total records

Functional annotation 1 EC 4 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

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.46. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.85. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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 (%): 34.118 Lower values reduce human off-target concern.
Human E-value: 3.25e-20
Gut microbiome similarity: 3.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 50.442 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 92.6 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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) 0.849

Structure A0A0H3GRD6

Pocket Pocket 1

Druggability (FPocket) 0.46

Structure A0A0H3GRD6

Pocket Pocket 21

ColabFold model

P2Rank 0.657 · Pocket 1

FPocket 0.318 · Pocket 3

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 177 / 4744 genomes with a hit

Prevalence 3.7%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Relative network centrality 0.0% more central than 0.0% of genes in this genome

Chokepoint Not a chokepoint

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MPNSLTWCDLPEDVSLWPGLPLSLSGDEVMPLDYHAGRSGWLLYGRGLDKRRLTAWQRELGAALVIVASWVVEDYQVIRLAGSLTPRATRLAHEAGLDVAPLGKIPHLRTPGLLVMDMDSTAIQIECIDEIAKLAGTGELVSEVTERAMRGELDFTASLRQRVATLKDADASILLQVRDALPLMPGLAQLVLKLETLGWKVAIASGGFTFFAEYLRDKLHLDAVFANELEIRDGKLTGNVLGDIVDAKYKANTLRKLAEKYEIPTAQTVAIGDGANDLPMIKAAGLGIAYHAKPKVNEQAEVTIRHADLMGVFCILSGSMNQK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

3.1.3.3

Gene Ontology (GO)

GO:0006564 The chemical reactions and pathways resulting in the formation of L-serine.
GO:0036424 Catalysis of the reaction: O-phospho-L-serine + H2O = L-serine + phosphate, on a free amino acid.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0000287 Binding to a magnesium (Mg) ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
113	292	CDD	cd07500	HAD_PSP
170	316	FunFam	G3DSA:3.40.50.1000:FF:000048	Phosphoserine phosphatase
89	315	PANTHER	PTHR43344	PHOSPHOSERINE PHOSPHATASE
37	100	Pfam	PF18429	Domain of unknown function (DUF5609)
37	100	InterPro	IPR041449	Phosphoserine phosphatase, N-terminal
113	284	NCBIfam	TIGR01488	HAD-IB family phosphatase
107	319	SFLD	SFLDG01136	C1.6: Phosphoserine Phosphatase Like
98	316	NCBIfam	TIGR00338	phosphoserine phosphatase SerB
98	316	InterPro	IPR004469	Phosphoserine phosphatase
36	322	Gene3D	G3DSA:3.30.70.2020	-
117	281	Pfam	PF12710	haloacid dehalogenase-like hydrolase
121	183	FunFam	G3DSA:1.10.150.210:FF:000001	Phosphoserine phosphatase
107	316	Gene3D	G3DSA:3.40.50.1000	-
107	316	InterPro	IPR023214	HAD superfamily
107	319	SFLD	SFLDF00029	phosphoserine phosphatase
107	319	InterPro	IPR004469	Phosphoserine phosphatase
121	183	Gene3D	G3DSA:1.10.150.210	Phosphoserine phosphatase; domain 2
110	317	SUPERFAMILY	SSF56784	HAD-like
110	317	InterPro	IPR036412	HAD-like superfamily

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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Drag to rotate — click the view, then scroll to zoom.

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

0.849

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Surrounding area

Pocket 2 P2Rank #2

0.006

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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 #21

0.46

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Surrounding area

Pocket 2 FPocket #5

0.344

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Surrounding area

Residue sets

UniProt: Active site:117-117 Nucleophile

UniProt: Active site:119-119 Proton donor

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.657

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Surrounding area

Pocket 2 P2Rank #2

0.053

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Surrounding area

Pocket 3 P2Rank #3

0.037

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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_A0A0H3GRD6	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_2588	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.

57 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 7 records from similar proteins

Structural ligands 7 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

1PS PDB via homolog 201.2 Da · LogP -0.09 · TPSA 61.1 Open detail RCSB PDB

AF3 PDB via homolog Detail RCSB PDB

ALF PDB via homolog Detail RCSB PDB

APO PDB via homolog Detail RCSB PDB

HJT 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
1PS RCSB PDB	4AP9	B6YX36	201.2 Da LogP -0.09 TPSA 61.1	✓ Ro5	✓ Clean	`c1cc[n+](cc1)CCCS(=O)(=O)[O-]`
AF3 RCSB PDB	1L7N	Q58989	84.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`F[Al](F)F`
ALF RCSB PDB	1L7N	Q58989	103.0 Da LogP 1.30 TPSA 0.0	✓ Ro5	✓ Clean	`F[Al-](F)(F)F`
APO RCSB PDB	1L8L	P78330	169.1 Da LogP -1.42 TPSA 120.8	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)N)P(=O)(O)O`
HJT RCSB PDB	6Q6J	P78330	183.2 Da LogP -1.32 TPSA 117.7	✓ Ro5	✓ Clean	`C(CS(=O)(=O)O)[C@@H](C(=O)O)N`
PG0 RCSB PDB	5JLP	A0QJI1	120.1 Da LogP -0.36 TPSA 38.7	✓ Ro5	✓ Clean	`COCCOCCO`
SEP RCSB PDB	6HYJ	P78330	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).

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`
ZINC1857524240 ZINC	0.652	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`COCCNCCOCCOCCO`
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`
ZINC1530285 ZINC	0.613	254.3 Da LogP -1.82 TPSA 146.8	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)NCCS(=O)(=O)O)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`
ZINC4831627 ZINC	0.593	370.5 Da LogP -0.21 TPSA 76.0	✓ Ro5	✓ Clean	`O=S(=O)(CC[n+]1ccccc1)CCS(=O)(=O)CC[n+]1ccccc1`
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`
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`
ZINC1579976 ZINC	0.567	243.3 Da LogP -0.59 TPSA 117.7	✓ Ro5	✓ Clean	`N[C@H](CSCCCS(=O)(=O)O)C(=O)O`
ZINC22112620 ZINC	0.567	216.3 Da LogP 0.64 TPSA 58.3	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCC[n+]1ccccc1`
ZINC5501912 ZINC	0.567	243.3 Da LogP -0.59 TPSA 117.7	✓ Ro5	✓ Clean	`N[C@@H](CSCCCS(=O)(=O)O)C(=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`
ZINC34764844 ZINC	0.550	206.3 Da LogP 1.09 TPSA 36.9	✓ Ro5	✓ Clean	`CCCOCCOCCOCCOC`
ZINC3872193 ZINC	0.548	240.2 Da LogP -1.86 TPSA 146.8	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)NCS(=O)(=O)O)C(=O)O`
ZINC1644613 ZINC	0.545	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC1634282 ZINC	0.542	214.3 Da LogP 1.74 TPSA 7.8	✓ Ro5	✓ Clean	`c1cc[n+](CCCC[n+]2ccccc2)cc1`
ZINC2383745924 ZINC	0.542	398.5 Da LogP -0.01 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCC(CO)COCCOCCOCCOC`
ZINC390794 ZINC	0.542	200.3 Da LogP 1.35 TPSA 7.8	✓ Ro5	✓ Clean	`c1cc[n+](CCC[n+]2ccccc2)cc1`
ZINC13537595 ZINC	0.533	208.3 Da LogP 0.25 TPSA 104.2	✓ Ro5	✓ Clean	`CCC[S@](=N)(=O)CC[C@H](N)C(=O)O`
ZINC1579929 ZINC	0.533	208.3 Da LogP 0.25 TPSA 104.2	✓ Ro5	✓ Clean	`CCC[S@@](=N)(=O)CC[C@@H](N)C(=O)O`
ZINC17130070 ZINC	0.533	208.3 Da LogP 0.25 TPSA 104.2	✓ Ro5	✓ Clean	`CCC[S@](=N)(=O)CC[C@@H](N)C(=O)O`
ZINC3651794 ZINC	0.533	208.3 Da LogP 0.25 TPSA 104.2	✓ Ro5	✓ Clean	`CCC[S@@](=N)(=O)CC[C@H](N)C(=O)O`
ZINC5784111 ZINC	0.533	223.3 Da LogP 0.00 TPSA 97.5	✓ Ro5	✓ Clean	`CCCCS(=O)(=O)CC[C@H](N)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.

Cross-references

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

Sequence

UniProt A0A0H3GRD6

Pathways

BioCyc PSERPHOSPHA-RXN BioCyc RXN0-5114[CCO-CYTOSOL]-3-P-SERINE/WATER//SER/Pi.38. BioCyc RXN0-5114[CCO-PERI-BAC]-3-P-SERINE/WATER//SER/Pi.39.