Protein profile

PA4602

serine hydroxymethyltransferase

Genome: NC_002516.2

Gene: PA4602 glyA3 Structure source: AlphaFold UniProt Q9HVI7
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Amino acids 417
Annotations 8
Features 21
PDB binders 11
Druggability 0.838

Overview

Basic information about this protein and its source genome.

Accession
PA4602
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA4602 glyA3
Status
annotated
Amino acids
417
Structure source
AlphaFold
EC
2.1.2.1
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. 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:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. GO:0019264 OBSOLETE. The chemical reactions and pathways resulting in the formation of glycine from L-serine. GO:0035999 The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesize other tetrahydrofolate molecules. GO:0046653 The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
53.846
Human E-value
7.38e-12
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 0.838
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • 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:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0019264 OBSOLETE. The chemical reactions and pathways resulting in the formation of glycine from L-serine.
  • GO:0035999 The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesize other tetrahydrofolate molecules.
  • GO:0046653 The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
9 385 Pfam PF00464 Serine hydroxymethyltransferase
9 385 InterPro IPR039429 Serine hydroxymethyltransferase-like domain
11 415 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
11 415 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
16 36 Coils Coil Coil
37 279 Gene3D G3DSA:3.40.640.10 -
37 279 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
7 416 Hamap MF_00051 Serine hydroxymethyltransferase [glyA].
7 416 InterPro IPR001085 Serine hydroxymethyltransferase
8 388 PANTHER PTHR11680 SERINE HYDROXYMETHYLTRANSFERASE
8 388 InterPro IPR001085 Serine hydroxymethyltransferase
37 279 FunFam G3DSA:3.40.640.10:FF:000001 Serine hydroxymethyltransferase
6 416 SUPERFAMILY SSF53383 PLP-dependent transferases
6 416 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
221 237 ProSitePatterns PS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.
221 237 InterPro IPR019798 Serine hydroxymethyltransferase, pyridoxal phosphate binding site
273 415 FunFam G3DSA:3.90.1150.10:FF:000003 Serine hydroxymethyltransferase
2 417 PIRSF PIRSF000412 SHMT
2 417 InterPro IPR001085 Serine hydroxymethyltransferase
9 408 CDD cd00378 SHMT
9 408 InterPro IPR001085 Serine hydroxymethyltransferase

3D Structure

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

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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 PA4602
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 0.261

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.

61 records

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
4WXG
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
2VMX
Q7SIB6 119.1 Da LogP -1.22 TPSA 83.5 ✓ Ro5 ✓ Clean C[C@@H]([C@@H](C(=O)O)N)O
CAC
4WXB
Q5M0B4 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[O-]
DTH
6TI3
Q5M0B4 119.1 Da LogP -1.22 TPSA 83.5 ✓ Ro5 ✓ Clean C[C@@H]([C@H](C(=O)O)N)O
EVM
6TGH
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
1DFO
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
1KL2
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
6YMD
I7H6W6 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PLG
1DFO
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
6YMF
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
6YMD
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.