Protein profile

PA5302

alanine racemase

Genome: NC_002516.2

Gene: dadX PA5302 Structure source: Experimental + AlphaFold UniProt Q9HTQ2
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Amino acids 357
Annotations 7
Features 42
PDB binders 5
Druggability 0.612

Overview

Basic information about this protein and its source genome.

Accession
PA5302
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
dadX PA5302
Status
annotated
Amino acids
357
Structure source
Experimental + AlphaFold
EC
5.1.1.1
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:0008784 Catalysis of the reaction: L-alanine = D-alanine. 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:0030632 The chemical reactions and pathways resulting in the formation of D-alanine, the D-enantiomer of the amino acid alanine, i.e (2R)-2-aminopropanoic acid. 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:0006522 OBSOLETE. The chemical reactions and pathways involving alanine, 2-aminopropanoic acid.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
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 0.612
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008784 Catalysis of the reaction: L-alanine = D-alanine.
  • 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:0030632 The chemical reactions and pathways resulting in the formation of D-alanine, the D-enantiomer of the amino acid alanine, i.e (2R)-2-aminopropanoic acid.
  • 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:0006522 OBSOLETE. The chemical reactions and pathways involving alanine, 2-aminopropanoic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

42 records
Show feature table
Start End DB Term Name
3 354 NCBIfam TIGR00492 alanine racemase
3 354 InterPro IPR000821 Alanine racemase
232 355 SMART SM01005 Ala_racemase_C_2
232 355 InterPro IPR011079 Alanine racemase, C-terminal
232 354 Pfam PF00842 Alanine racemase, C-terminal domain
232 354 InterPro IPR011079 Alanine racemase, C-terminal
212 356 FunFam G3DSA:2.40.37.10:FF:000002 Alanine racemase
10 211 Gene3D G3DSA:3.20.20.10 Alanine racemase
10 211 InterPro IPR029066 PLP-binding barrel
3 354 CDD cd06827 PLPDE_III_AR_proteobact
10 214 FunFam G3DSA:3.20.20.10:FF:000002 Alanine racemase
3 355 Hamap MF_01201 Alanine racemase.
3 355 InterPro IPR000821 Alanine racemase
30 40 ProSitePatterns PS00395 Alanine racemase pyridoxal-phosphate attachment site.
30 40 InterPro IPR020622 Alanine racemase, pyridoxal-phosphate attachment site
228 355 SUPERFAMILY SSF50621 Alanine racemase C-terminal domain-like
228 355 InterPro IPR009006 Alanine racemase/group IV decarboxylase, C-terminal
265 280 PRINTS PR00992 Alanine racemase signature
265 280 InterPro IPR000821 Alanine racemase
338 351 PRINTS PR00992 Alanine racemase signature
338 351 InterPro IPR000821 Alanine racemase
120 132 PRINTS PR00992 Alanine racemase signature
120 132 InterPro IPR000821 Alanine racemase
248 263 PRINTS PR00992 Alanine racemase signature
248 263 InterPro IPR000821 Alanine racemase
154 165 PRINTS PR00992 Alanine racemase signature
154 165 InterPro IPR000821 Alanine racemase
191 218 PRINTS PR00992 Alanine racemase signature
191 218 InterPro IPR000821 Alanine racemase
60 78 PRINTS PR00992 Alanine racemase signature
60 78 InterPro IPR000821 Alanine racemase
286 303 PRINTS PR00992 Alanine racemase signature
286 303 InterPro IPR000821 Alanine racemase
25 41 PRINTS PR00992 Alanine racemase signature
25 41 InterPro IPR000821 Alanine racemase
212 357 Gene3D G3DSA:2.40.37.10 Lyase, Ornithine Decarboxylase; Chain A, domain 1
212 357 InterPro IPR009006 Alanine racemase/group IV decarboxylase, C-terminal
1 355 PANTHER PTHR30511 ALANINE RACEMASE
8 218 Pfam PF01168 Alanine racemase, N-terminal domain
8 218 InterPro IPR001608 Alanine racemase, N-terminal
8 233 SUPERFAMILY SSF51419 PLP-binding barrel
8 233 InterPro IPR029066 PLP-binding barrel

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

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 1RCQ
X-ray 1.45 Å A
100.0% 1-357
PDBe RCSB PDBj File
Viewing
AlphaFold PA5302
AlphaFold — — 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
3 0.612
4 0.418

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 24.47 0.899
2 4.49 0.191
3 1.71 0.03
4 1.6 0.025
5 1.53 0.023

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.

55 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
BEZ
3S46
P0A2W8 122.1 Da LogP 1.38 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)O
DCS
5FAJ
O86786 333.2 Da LogP -0.78 TPSA 150.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CONC2=O)O
IN5
4XBJ
P0A6B4 356.2 Da LogP 0.32 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](C)P(=O)(O)O)O
MLI
6A2F
Q9HUN4 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PPI
5FAG
O86786 74.1 Da LogP 0.48 TPSA 37.3 ✓ Ro5 ✓ Clean CCC(=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.