Protein profile

PA4960

phosphoserine phosphatase

Genome: NC_002516.2

Gene: PA4960 Structure source: AlphaFold UniProt Q9HUK5

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Amino acids 429

Annotations 5

Features 25

PDB binders 7

Druggability 0.55

Overview

Basic information about this protein and its source genome.

Accession: PA4960
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4960
Status: annotated
Amino acids: 429
Structure source: AlphaFold

3.1.3.3

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

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 36.686
Human E-value: 9.000000000000001e-21
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.55

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

3.1.3.3

Gene Ontology (GO)

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

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records

Show feature table

Start	End	DB	Term	Name
217	396	CDD	cd07500	HAD_PSP
216	422	SUPERFAMILY	SSF56784	HAD-like
216	422	InterPro	IPR036412	HAD-like superfamily
195	420	PANTHER	PTHR43344	PHOSPHOSERINE PHOSPHATASE
217	387	NCBIfam	TIGR01488	HAD-IB family phosphatase
214	429	FunFam	G3DSA:3.40.50.1000:FF:000041	Phosphoserine phosphatase SerB
211	426	SFLD	SFLDF00029	phosphoserine phosphatase
211	426	InterPro	IPR004469	Phosphoserine phosphatase
31	106	ProSiteProfiles	PS51671	ACT domain profile.
31	106	InterPro	IPR002912	ACT domain
202	420	NCBIfam	TIGR00338	phosphoserine phosphatase SerB
202	420	InterPro	IPR004469	Phosphoserine phosphatase
27	108	SUPERFAMILY	SSF55021	ACT-like
27	108	InterPro	IPR045865	ACT-like domain
121	213	FunFam	G3DSA:3.30.70.260:FF:000065	Phosphoserine phosphatase SerB
28	110	FunFam	G3DSA:3.30.70.260:FF:000041	Phosphoserine phosphatase SerB
28	104	Pfam	PF13740	ACT domain
214	428	Gene3D	G3DSA:3.40.50.1000	-
214	428	InterPro	IPR023214	HAD superfamily
28	110	Gene3D	G3DSA:3.30.70.260	-
31	105	CDD	cd04870	ACT_PSP_1
211	426	SFLD	SFLDS00003	Haloacid Dehalogenase
121	213	Gene3D	G3DSA:3.30.70.260	-
124	207	CDD	cd04871	ACT_PSP_2
218	385	Pfam	PF12710	haloacid dehalogenase-like hydrolase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA4960	AlphaFold	—	—	full sequence	—	Viewing

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
4				0.55

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

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, 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	4AP9	B6YX36	201.2 Da LogP -0.09 TPSA 61.1	✓ Ro5	✓ Clean	`c1cc[n+](cc1)CCCS(=O)(=O)[O-]`
AF3	1L7N	Q58989	84.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`F[Al](F)F`
ALF	1L7N	Q58989	103.0 Da LogP 1.30 TPSA 0.0	✓ Ro5	✓ Clean	`F[Al-](F)(F)F`
APO	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	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	5JLP	A0QJI1	120.1 Da LogP -0.36 TPSA 38.7	✓ Ro5	✓ Clean	`COCCOCCO`
SEP	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	1.000	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	1.000	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	1.000	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	1.000	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	1.000	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	1.000	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	1.000	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC575419714	0.727	312.4 Da LogP 0.42 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCSCCOCCOCCO`
ZINC115163232	0.700	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCCO`
ZINC258837490	0.700	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCCO`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1692489	0.688	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC3874716	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC4530388	0.688	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5178829	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5701172	0.688	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC5997861	0.688	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC575432150	0.667	344.4 Da LogP -0.89 TPSA 100.5	✓ Ro5	✓ Clean	`COCCOCCOCCS(=O)(=O)CCOCCOCCO`
ZINC1857524240	0.652	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`COCCNCCOCCOCCO`
ZINC197248777	0.621	213.1 Da LogP -1.01 TPSA 119.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@H](N)COP(=O)(O)O`
ZINC197248785	0.621	213.1 Da LogP -1.01 TPSA 119.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@@H](N)COP(=O)(O)O`
ZINC1530285	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	0.600	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	0.600	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4831627	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	0.583	222.2 Da LogP -0.80 TPSA 74.2	✓ Ro5	✓ Clean	`COC(=O)COCCOCCOCCO`
ZINC1857790631	0.583	280.3 Da LogP -0.39 TPSA 83.5	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCOCCO`
ZINC196151418	0.583	266.3 Da LogP -0.78 TPSA 83.5	✓ Ro5	✓ Clean	`COC(=O)COCCOCCOCCOCCO`
ZINC202958272	0.583	236.3 Da LogP -0.41 TPSA 74.2	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCO`
ZINC34111591	0.583	207.3 Da LogP -1.06 TPSA 62.2	✓ Ro5	✓ Clean	`COCCOCCN(CCO)CCO`
ZINC642881862	0.583	324.4 Da LogP -0.38 TPSA 92.7	✓ Ro5	✓ Clean	`COC(=O)CCOCCOCCOCCOCCOCCO`
ZINC1579976	0.567	243.3 Da LogP -0.59 TPSA 117.7	✓ Ro5	✓ Clean	`N[C@H](CSCCCS(=O)(=O)O)C(=O)O`
ZINC22112620	0.567	216.3 Da LogP 0.64 TPSA 58.3	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCC[n+]1ccccc1`
ZINC5501912	0.567	243.3 Da LogP -0.59 TPSA 117.7	✓ Ro5	✓ Clean	`N[C@@H](CSCCCS(=O)(=O)O)C(=O)O`
ZINC3869233	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	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	0.550	206.3 Da LogP 1.09 TPSA 36.9	✓ Ro5	✓ Clean	`CCCOCCOCCOCCOC`
ZINC3872193	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	0.545	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC1634282	0.542	214.3 Da LogP 1.74 TPSA 7.8	✓ Ro5	✓ Clean	`c1cc[n+](CCCC[n+]2ccccc2)cc1`
ZINC2383745924	0.542	398.5 Da LogP -0.01 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCC(CO)COCCOCCOCCOC`
ZINC390794	0.542	200.3 Da LogP 1.35 TPSA 7.8	✓ Ro5	✓ Clean	`c1cc[n+](CCC[n+]2ccccc2)cc1`
ZINC13537595	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	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	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	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	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.