Protein profile

VK055_2588

phosphoserine phosphatase SerB

Genome: KpATCC43816

Gene: serB AIK81185.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GRD6

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Amino acids 323

Annotations 5

Features 19

PDB binders 7

Druggability 0.46

Overview

Basic information about this protein and its source genome.

Accession: VK055_2588
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: serB AIK81185.1
Status: annotated
Amino acids: 323
Structure source: AlphaFold + ColabFold

3.1.3.3

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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 34.118
Human E-value: 3.25e-20
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 50.442
Localization: Cytoplasmic
ColabFold pLDDT: 92.6

Selected Druggability evidence

AlphaFold / UniProt model

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 0.46

Structure A0A0H3GRD6

Pocket Pocket 21

P2Rank 0.849

Structure A0A0H3GRD6

Pocket Pocket 1

ColabFold model

FPocket 0.318 · Pocket 3

P2Rank 0.657 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 177 / 4744 genomes with a hit

Normalized 0.037

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: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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GRD6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_2588	ColabFold	—	—	full sequence	—	Loaded

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
21				0.46
20				0.008
4				0.0
11				0.0

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				24.07	0.849
2				1.06	0.006

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
2				0.026
6				0.022
18				0.0
19				0.0

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	14.92	0.657
2	2.43	0.053
3	2.02	0.037

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.