Protein profile

KP13_01549

Alanine racemase, catabolic

Genome: KpKP13

Gene: dadB AHE43922.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GUM6
Export view
Amino acids 356
Annotations 8
Features 41
PDB binders 5
Druggability 0.121

Overview

Basic information about this protein and its source genome.

Accession
KP13_01549
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
dadB AHE43922.1
Status
annotated
Amino acids
356
Structure source
AlphaFold + ColabFold
EC
5.1.1.1
GO
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.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
44.034
DEG E-value
1.81e-96
Localization
Cytoplasmic
ColabFold pLDDT
97.64

Selected Druggability evidence

AlphaFold / UniProt model

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 0.121
Structure A0A0H3GUM6
Pocket Pocket 4
P2Rank 0.88
Structure A0A0H3GUM6
Pocket Pocket 1
ColabFold model
FPocket 0.369 · Pocket 7
P2Rank 0.854 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 116 / 4744 genomes with a hit
Normalized 0.024

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: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 Features

Domain/signature hits from InterPro and related databases.

41 records
Show feature table
Start End DB Term Name
32 42 ProSitePatterns PS00395 Alanine racemase pyridoxal-phosphate attachment site.
32 42 InterPro IPR020622 Alanine racemase, pyridoxal-phosphate attachment site
3 354 PANTHER PTHR30511 ALANINE RACEMASE
211 356 FunFam G3DSA:2.40.37.10:FF:000002 Alanine racemase
232 354 Pfam PF00842 Alanine racemase, C-terminal domain
232 354 InterPro IPR011079 Alanine racemase, C-terminal
4 356 NCBIfam TIGR00492 alanine racemase
4 356 InterPro IPR000821 Alanine racemase
27 43 PRINTS PR00992 Alanine racemase signature
27 43 InterPro IPR000821 Alanine racemase
190 217 PRINTS PR00992 Alanine racemase signature
190 217 InterPro IPR000821 Alanine racemase
286 303 PRINTS PR00992 Alanine racemase signature
286 303 InterPro IPR000821 Alanine racemase
338 351 PRINTS PR00992 Alanine racemase signature
338 351 InterPro IPR000821 Alanine racemase
61 79 PRINTS PR00992 Alanine racemase signature
61 79 InterPro IPR000821 Alanine racemase
248 263 PRINTS PR00992 Alanine racemase signature
248 263 InterPro IPR000821 Alanine racemase
121 133 PRINTS PR00992 Alanine racemase signature
121 133 InterPro IPR000821 Alanine racemase
155 166 PRINTS PR00992 Alanine racemase signature
155 166 InterPro IPR000821 Alanine racemase
265 280 PRINTS PR00992 Alanine racemase signature
265 280 InterPro IPR000821 Alanine racemase
227 354 SUPERFAMILY SSF50621 Alanine racemase C-terminal domain-like
227 354 InterPro IPR009006 Alanine racemase/group IV decarboxylase, C-terminal
9 217 Pfam PF01168 Alanine racemase, N-terminal domain
9 217 InterPro IPR001608 Alanine racemase, N-terminal
4 356 Hamap MF_01201 Alanine racemase.
9 233 SUPERFAMILY SSF51419 PLP-binding barrel
9 233 InterPro IPR029066 PLP-binding barrel
232 356 SMART SM01005 Ala_racemase_C_2
232 356 InterPro IPR011079 Alanine racemase, C-terminal
12 210 Gene3D G3DSA:3.20.20.10 Alanine racemase
12 210 InterPro IPR029066 PLP-binding barrel
4 354 CDD cd06827 PLPDE_III_AR_proteobact
11 213 FunFam G3DSA:3.20.20.10:FF:000002 Alanine racemase
211 355 Gene3D G3DSA:2.40.37.10 Lyase, Ornithine Decarboxylase; Chain A, domain 1
211 355 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; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GUM6
AlphaFold — — full sequence — Viewing
ColabFold KP13_01549
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 16.08 0.769
2 1.87 0.037
3 1.85 0.036

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.