Protein target profile

KP13_00831

Serine hydroxymethyltransferase

Genome: KpKP13 Gene: glyA AHE43195.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRS5
Length 419
Pocket druggability 0.418
Direct ligand evidence 0 62 total records
Functional annotation 0 EC 5 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.

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 (%)
57.031 Lower values reduce human off-target concern.
Human E-value
6.949999999999999e-42
Gut microbiome similarity
66.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
97.602 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
98.27 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.418
Structure A0A0H3GRS5
Pocket Pocket 6
P2Rank 0.829
Structure A0A0H3GRS5
Pocket Pocket 1
ColabFold model
FPocket 0.449 · Pocket 7
P2Rank 0.727 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3140 / 4744 genomes with a hit
Prevalence 66.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MRMLKREMNIADYDAELWQAMEQEKVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYPGKRYYGGCEYVDVVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLQPGDTVLGMNLAQGGHLTHGSPVNFSGKLYNIIPYGIDESGKIDYDDMAKQAQEHKPKMIIGGFSAYSGIVDWAKMREIADSIGAYLFVDMAHVAGLIAAGVYPNPVPHAHVVTTTTHKTLAGPRGGLILAKGGSEELYKKLNSAVFPSAQGGPLMHVIAAKAVALKEAMEPEFKVYQQQVAKNAKAMVEVFLNRGYKVVSGGTENHLFLLDLVDKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTSGIRIGSPAVTRRGFKEAEVKELAGWMCDVLDNINDDAVIERVKGKVLDICARFPVYA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0035999 The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesize other tetrahydrofolate molecules.
  • GO:0004372 Catalysis of the reaction: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine.
  • 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:0019264 OBSOLETE. The chemical reactions and pathways resulting in the formation of glycine from L-serine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
216 419 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
11 411 CDD cd00378 SHMT
11 411 InterPro IPR001085 Serine hydroxymethyltransferase
11 388 Pfam PF00464 Serine hydroxymethyltransferase
11 388 InterPro IPR039429 Serine hydroxymethyltransferase-like domain
272 418 FunFam G3DSA:3.90.1150.10:FF:000003 Serine hydroxymethyltransferase
8 418 SUPERFAMILY SSF53383 PLP-dependent transferases
8 418 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
13 418 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
13 418 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
195 215 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
9 419 Hamap MF_00051 Serine hydroxymethyltransferase [glyA].
9 419 InterPro IPR001085 Serine hydroxymethyltransferase
1 419 PIRSF PIRSF000412 SHMT
1 419 InterPro IPR001085 Serine hydroxymethyltransferase
223 239 ProSitePatterns PS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.
223 239 InterPro IPR019798 Serine hydroxymethyltransferase, pyridoxal phosphate binding site
8 392 PANTHER PTHR11680 SERINE HYDROXYMETHYLTRANSFERASE
8 392 InterPro IPR001085 Serine hydroxymethyltransferase
39 282 FunFam G3DSA:3.40.640.10:FF:000001 Serine hydroxymethyltransferase
1 194 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
39 282 Gene3D G3DSA:3.40.640.10 -
39 282 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major 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 #6
0.418
Likely same site as P2Rank 1 3.7 Å 12 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #20
0.27
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Surrounding area
Site 3 FPocket #3
0.241
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Surrounding area
Site 4 FPocket #22
0.225
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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
0.829
Likely same site as FPocket 6 3.7 Å 12 shared residues 100% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.055
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Surrounding area
Site 3 P2Rank #3
0.014
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Surrounding area
Site 4 P2Rank #4
0.001
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Surrounding area
Residue sets
UniProt: Binding site:121-121
UniProt: Binding site:125-127
UniProt: Binding site:246-246
UniProt: Binding site:355-357
UniProt: Site:228-228 Plays an important role in substrate specificity
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_A0A0H3GRS5
AlphaFold DB full sequence Viewing
ColabFold KP13_00831
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.

62 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 12 records from similar proteins
Structural ligands 12 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2BO PDB via homolog 350.3 Da · LogP -0.37 · TPSA 169.4 Open detail RCSB PDB
ALO PDB via homolog Detail RCSB PDB
CAC PDB via homolog Detail RCSB PDB
DTH PDB via homolog Detail RCSB PDB
EVM PDB via homolog Detail RCSB PDB

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
2BO RCSB PDB Q5M0B4 350.3 Da LogP -0.37 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]([C@@H](C)O)C(…
ALO RCSB PDB Q7SIB6 119.1 Da LogP -1.22 TPSA 83.5 ✓ Ro5 ✓ Clean C[C@@H]([C@@H](C(=O)O)N)O
CAC RCSB PDB Q5M0B4 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[O-]
DTH RCSB PDB Q5M0B4 119.1 Da LogP -1.22 TPSA 83.5 ✓ Ro5 ✓ Clean C[C@@H]([C@H](C(=O)O)N)O
EVM RCSB PDB Q5M0B4 333.2 Da LogP -0.27 TPSA 169.8 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C-](CO)C(=O)O)O
FFO RCSB PDB P0A825 473.4 Da LogP -0.73 TPSA 219.8 1 viol. ✓ Clean c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2C…
FON RCSB PDB Q7SIB6 473.4 Da LogP -0.73 TPSA 219.8 1 viol. ✓ Clean c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@@H]2…
MLI RCSB PDB I7H6W6 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
O3Z RCSB PDB Q5M4W1 336.2 Da LogP -0.76 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CO)C(=O)O)O
PLG RCSB PDB P0A825 306.2 Da LogP -0.12 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O
PLS RCSB PDB I7H6W6 336.2 Da LogP -0.76 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CO)C(=O)O)O
PMP RCSB PDB I7H6W6 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)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.