Protein profile

VK055_1549

phosphoserine transaminase

Genome: KpATCC43816

Gene: AIK80169.1 serC Structure source: Experimental + ColabFold UniProt A6T700

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Amino acids 362

Annotations 3

Features 21

PDB binders 3

Druggability 0.699

Overview

Basic information about this protein and its source genome.

Accession: VK055_1549
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK80169.1 serC
Status: annotated
Amino acids: 362
Structure source: Experimental + ColabFold

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:0004648 Catalysis of the reaction: O-phospho-L-serine + 2-oxoglutarate = 3-phosphonooxypyruvate + L-glutamate. 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 (%): 47.814
Human E-value: 1.14e-118
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 65.738
DEG E-value: 7.58e-172
Localization: Cytoplasmic
ColabFold pLDDT: 98.03

Selected Druggability evidence

PDB experimental structure

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 0.699

Structure 7T7J

Pocket Pocket 3

P2Rank 0.763

Structure 7T7J

Pocket Pocket 1

ColabFold model

FPocket 0.846 · Pocket 1

P2Rank 0.485 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 252 / 4744 genomes with a hit

Normalized 0.053

Sequence

Primary amino-acid sequence viewer.

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:0004648 Catalysis of the reaction: O-phospho-L-serine + 2-oxoglutarate = 3-phosphonooxypyruvate + L-glutamate.
GO:0006564 The chemical reactions and pathways resulting in the formation of L-serine.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
189	208	ProSitePatterns	PS00595	Aminotransferases class-V pyridoxal-phosphate attachment site.
189	208	InterPro	IPR020578	Aminotransferase class-V, pyridoxal-phosphate binding site
1	362	PIRSF	PIRSF000525	SerC
1	362	InterPro	IPR022278	Phosphoserine aminotransferase
259	362	FunFam	G3DSA:3.90.1150.10:FF:000006	Phosphoserine aminotransferase
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
3	362	SUPERFAMILY	SSF53383	PLP-dependent transferases
3	362	InterPro	IPR015424	Pyridoxal phosphate-dependent transferase
16	258	FunFam	G3DSA:3.40.640.10:FF:000010	Phosphoserine aminotransferase
5	359	CDD	cd00611	PSAT_like
5	359	InterPro	IPR022278	Phosphoserine aminotransferase
2	361	Hamap	MF_00160	Phosphoserine aminotransferase [serC].
2	361	InterPro	IPR022278	Phosphoserine aminotransferase
2	361	PANTHER	PTHR43247	PHOSPHOSERINE AMINOTRANSFERASE
4	361	NCBIfam	TIGR01364	phosphoserine transaminase
4	361	InterPro	IPR022278	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; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

1 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 7T7J	X-ray	20.00 Å	-	—	PDBe RCSB PDBj File	Viewing
ColabFold VK055_1549	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				0.569
18				0.542
2				0.225

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	56.24	0.985
2	49.54	0.979
3	6.53	0.33
4	5.03	0.229
5	3.29	0.115

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
1				0.846

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	5.35	0.253
2	2.54	0.071
3	1.19	0.01

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

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
GAM	1BJO	P23721	161.2 Da LogP -0.35 TPSA 100.6	✓ Ro5	✓ Clean	`C[C@](CCC(=O)O)(C(=O)O)N`
PMP	6CZY	Q96255	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CN)O`
SEP	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	Q9Y617	6.58	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	1.000	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CN)c1O`
ZINC1532705	0.769	249.2 Da LogP 0.20 TPSA 120.1	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CO)c1O`
ZINC1656021	0.692	233.2 Da LogP 1.01 TPSA 99.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C)c1O`
ZINC1532514	0.643	247.1 Da LogP 0.52 TPSA 117.0	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C=O)c1O`
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`
ZINC64219269	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	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	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	0.583	218.2 Da LogP 0.81 TPSA 111.9	✓ Ro5	✓ Clean	`CC(CCC(=O)O)(CCC(=O)O)C(=O)O`
ZINC1857358	0.565	247.2 Da LogP 0.28 TPSA 137.9	✓ Ro5	✓ Clean	`NC(CCC(=O)O)(CCC(=O)O)CCC(=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`
ZINC220133900	0.538	398.3 Da LogP 3.77 TPSA 85.1	✓ Ro5	✓ Clean	`Cc1nc2nc(-c3cccnc3)nn2cc1C(=O)Nc1cccc(C(F)(F)F)…`
ZINC100300547	0.536	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@@](C)(N)C(=O)O`
ZINC1652265	0.536	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`CCCCCCCCC[C@](C)(N)C(=O)O`
ZINC20148987	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	0.523	219.1 Da LogP -0.02 TPSA 118.6	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(N)n1`
ZINC2114966	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	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	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	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	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	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	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	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	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	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	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	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	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	0.500	216.2 Da LogP 1.31 TPSA 91.7	✓ Ro5	✓ Clean	`CC(=O)C(C)(CCC(=O)O)CCC(=O)O`
ZINC1712438	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	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	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	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	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	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.