KpKP13 Protein target profile

Alanine racemase, biosynthetic

Accession: KP13_00390

Gene: alr AHE46872.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GGW4
Length 359
Pocket druggability (P2Rank · AlphaFold DB model) 0.907
Direct ligand evidence 0 60 total records
Functional annotation 1 EC 7 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
No hit
Gut microbiome similarity
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
98.14 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.907
Structure A0A0H3GGW4
Pocket Pocket 1
Druggability (FPocket) 0.551
Structure A0A0H3GGW4
Pocket Pocket 22
ColabFold model
P2Rank 0.904 · Pocket 1
FPocket 0.596 · Pocket 28
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 145 / 4744 genomes with a hit
Prevalence 3.1%

Sequence

Primary amino-acid sequence viewer.

MQAATVVINRRALRHNLQRLRELAPASKLVAVVKANAYGHGLLETARTLTDADAFGVARLEEALRLRAGGIAQPILLLEGFFAAEDLAVIAAQRLHTAVHSPEQLAALEQADLPEPVTVWMKLDTGMHRLGVRPEEAEAFYQRLSQCKNVRQPVNVVSHFARADEPTCGATERQLDIFTTFTEGKPGLRSIAASGGILLWPQSHYDWVRPGIILYGVSPLDDRSTGRDFGCQPVMTLSSSLIAVREHKAGEPVGYGGTWISERDTRLGVVAMGYGDGYPRAAPSGTPVLVNGREVPIVGRVAMDMICVDLGPQAQDKAGDAVVLWGEGLPVERIAEITKVSAYELITRLTSRVAMKYFD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0006522 OBSOLETE. The chemical reactions and pathways involving alanine, 2-aminopropanoic acid.
  • GO:0008784 Catalysis of the reaction: L-alanine = D-alanine.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0042803 Binding to an identical protein to form a homodimer.
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

41 records
Show feature table
Start End DB Term Name
10 214 Gene3D G3DSA:3.20.20.10 Alanine racemase
10 214 InterPro IPR029066 PLP-binding barrel
3 358 Hamap MF_01201 Alanine racemase.
3 358 InterPro IPR000821 Alanine racemase
10 215 FunFam G3DSA:3.20.20.10:FF:000002 Alanine racemase
234 357 Pfam PF00842 Alanine racemase, C-terminal domain
234 357 InterPro IPR011079 Alanine racemase, C-terminal
8 219 Pfam PF01168 Alanine racemase, N-terminal domain
8 219 InterPro IPR001608 Alanine racemase, N-terminal
215 359 Gene3D G3DSA:2.40.37.10 Lyase, Ornithine Decarboxylase; Chain A, domain 1
215 359 InterPro IPR009006 Alanine racemase/group IV decarboxylase, C-terminal
31 41 ProSitePatterns PS00395 Alanine racemase pyridoxal-phosphate attachment site.
31 41 InterPro IPR020622 Alanine racemase, pyridoxal-phosphate attachment site
267 282 PRINTS PR00992 Alanine racemase signature
267 282 InterPro IPR000821 Alanine racemase
288 305 PRINTS PR00992 Alanine racemase signature
288 305 InterPro IPR000821 Alanine racemase
155 166 PRINTS PR00992 Alanine racemase signature
155 166 InterPro IPR000821 Alanine racemase
192 219 PRINTS PR00992 Alanine racemase signature
192 219 InterPro IPR000821 Alanine racemase
26 42 PRINTS PR00992 Alanine racemase signature
26 42 InterPro IPR000821 Alanine racemase
340 353 PRINTS PR00992 Alanine racemase signature
340 353 InterPro IPR000821 Alanine racemase
60 78 PRINTS PR00992 Alanine racemase signature
60 78 InterPro IPR000821 Alanine racemase
120 132 PRINTS PR00992 Alanine racemase signature
120 132 InterPro IPR000821 Alanine racemase
250 265 PRINTS PR00992 Alanine racemase signature
250 265 InterPro IPR000821 Alanine racemase
234 358 SMART SM01005 Ala_racemase_C_2
234 358 InterPro IPR011079 Alanine racemase, C-terminal
3 357 CDD cd06827 PLPDE_III_AR_proteobact
213 359 FunFam G3DSA:2.40.37.10:FF:000002 Alanine racemase
3 358 NCBIfam TIGR00492 alanine racemase
1 358 PANTHER PTHR30511 ALANINE RACEMASE
8 235 SUPERFAMILY SSF51419 PLP-binding barrel
8 235 InterPro IPR029066 PLP-binding barrel
228 358 SUPERFAMILY SSF50621 Alanine racemase C-terminal domain-like
228 358 InterPro IPR009006 Alanine racemase/group IV decarboxylase, C-terminal

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.907
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Surrounding area
Pocket 2 P2Rank #2
0.084
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Surrounding area
Pocket 3 P2Rank #3
0.015
Likely same site as FPocket 28 6.8 Å 3 shared residues 43% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.015
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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #22
0.551
Show in viewer
Surrounding area
Pocket 2 FPocket #28
0.548
Likely same site as P2Rank 3 6.8 Å 3 shared residues 43% of smaller site
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Surrounding area
Pocket 3 FPocket #18
0.493
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Surrounding area
Residue sets
UniProt: Active site:255-255 Proton acceptor; specific for L-alanine
UniProt: Active site:34-34 Proton acceptor; specific for D-alanine
UniProt: Binding site:129-129
UniProt: Binding site:303-303
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_A0A0H3GGW4
AlphaFold DB full sequence Viewing
ColabFold KP13_00390
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.

60 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 9 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CO2 PDB via homolog 44.0 Da · LogP -0.58 · TPSA 34.1 Open detail RCSB PDB
DCS PDB via homolog Detail RCSB PDB
IN5 PDB via homolog Detail RCSB PDB
L7N PDB via homolog Detail RCSB PDB
MLI 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
CO2 RCSB PDB P94494 44.0 Da LogP -0.58 TPSA 34.1 ✓ Ro5 ✓ Clean C(=O)=O
DCS RCSB PDB 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 RCSB PDB 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
L7N RCSB PDB P9WQA9 332.2 Da LogP -2.37 TPSA 152.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=[NH+]/[C@@H]2CONC2=…
MLI RCSB PDB Q9HUN4 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
OJQ RCSB PDB P9WQA9 332.2 Da LogP -0.21 TPSA 162.8 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)C[NH2+]c2conc2O)O
P4K RCSB PDB P9WQA9 662.8 Da LogP 0.23 TPSA 149.5 2 viol. ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
PPI RCSB PDB O86786 74.1 Da LogP 0.48 TPSA 37.3 ✓ Ro5 ✓ Clean CCC(=O)O
UAH RCSB PDB P94494 219.1 Da LogP 0.70 TPSA 99.9 ✓ Ro5 ✓ Clean Cc1c(cc(cn1)COP(=O)(O)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.

Cross-references

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