KpKP13 Protein target profile

D-alanine--D-alanine ligase B

Accession: KP13_01903

Gene: AHE46344.1 ddlB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GML6
Length 306
Pocket druggability (P2Rank · AlphaFold DB model) 0.96
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 8 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
3.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
95.46 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) 0.96
Structure A0A0H3GML6
Pocket Pocket 1
Druggability (FPocket) 0.886
Structure A0A0H3GML6
Pocket Pocket 10
ColabFold model
P2Rank 0.957 · Pocket 1
FPocket 0.712 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 152 / 4744 genomes with a hit
Prevalence 3.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MADKIAVLFGGTSAEREVSLNSGAAVLAGLREGGVDAHPVDPRDVDITQLKKQGFKKAFIALHGRGGEDGTLQGLLELIQLPYTGSGVMASAISMDKLRSKWLWQGAGLPVAPWVALTRAQFAAGLSTDVEQQIAALGLPVIIKPSREGSSVGMSKVSESCDLASALALAFQHDDEVLVEKWLSGPEFTVAIVGEEILPSIRIQAAGTFYDYEAKYLSDETQYFCPGFEDPARESAIQNLVLKAWNVLGCKGWGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRILDLAG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0008716 Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H+ + phosphate.
  • GO:0046872 Binding to a metal ion.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
  • GO:0009252 The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
  • GO:0008360 Any process that modulates the surface configuration of a cell.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
248 276 ProSitePatterns PS00844 D-alanine--D-alanine ligase signature 2.
248 276 InterPro IPR000291 D-alanine--D-alanine ligase/VANA/B/C, conserved site
85 305 Gene3D G3DSA:3.30.470.20 -
35 306 PIRSF PIRSF039102 Ddl/VanB
35 306 InterPro IPR005905 D-alanine--D-alanine ligase
1 45 PIRSF PIRSF039102 Ddl/VanB
1 45 InterPro IPR005905 D-alanine--D-alanine ligase
3 306 Hamap MF_00047 D-alanine--D-alanine ligase [ddl].
3 306 InterPro IPR005905 D-alanine--D-alanine ligase
3 96 SUPERFAMILY SSF52440 PreATP-grasp domain
3 96 InterPro IPR016185 Pre-ATP-grasp domain superfamily
103 302 Pfam PF07478 D-ala D-ala ligase C-terminus
103 302 InterPro IPR011095 D-alanine--D-alanine ligase, C-terminal
4 305 PANTHER PTHR23132 D-ALANINE--D-ALANINE LIGASE
1 84 Gene3D G3DSA:3.40.50.20 -
111 183 FunFam G3DSA:3.30.1490.20:FF:000007 D-alanine--D-alanine ligase
147 302 FunFam G3DSA:3.30.470.20:FF:000008 D-alanine--D-alanine ligase
112 183 Gene3D G3DSA:3.30.1490.20 -
112 183 InterPro IPR013815 ATP-grasp fold, subdomain 1
4 305 NCBIfam TIGR01205 D-alanine--D-alanine ligase
4 305 InterPro IPR005905 D-alanine--D-alanine ligase
63 74 ProSitePatterns PS00843 D-alanine--D-alanine ligase signature 1.
63 74 InterPro IPR000291 D-alanine--D-alanine ligase/VANA/B/C, conserved site
101 303 ProSiteProfiles PS50975 ATP-grasp fold profile.
101 303 InterPro IPR011761 ATP-grasp fold
97 302 SUPERFAMILY SSF56059 Glutathione synthetase ATP-binding domain-like
1 84 FunFam G3DSA:3.40.50.20:FF:000013 D-alanine--D-alanine ligase
4 86 Pfam PF01820 D-ala D-ala ligase N-terminus
4 86 InterPro IPR011127 D-alanine--D-alanine ligase, N-terminal 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 · P2Rank

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

Pocket 1 P2Rank #1
0.96
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.032
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #10
0.886 Unusual size
Show in viewer
Surrounding area
Pocket 2 FPocket #1
0.88
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:15-15
UniProt: Active site:150-150
UniProt: Active site:281-281
UniProt: Binding site:257-257
UniProt: Binding site:270-270
UniProt: Binding site:272-272
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_A0A0H3GML6
AlphaFold DB full sequence Viewing
ColabFold KP13_01903
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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ANP PDB via homolog 506.2 Da · LogP -2.06 · TPSA 281.9 Open detail RCSB PDB
DS0 PDB via homolog Detail RCSB PDB
G1L PDB via homolog Detail RCSB PDB
PHY PDB via homolog Detail RCSB PDB
POB 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
ANP RCSB PDB Q5H614 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DS0 RCSB PDB P07862 182.1 Da LogP -1.23 TPSA 114.4 ✓ Ro5 ✓ Clean C1[C@H](C(=NO1)OP(=O)(O)O)N
G1L RCSB PDB Q5HEB7 279.7 Da LogP 3.91 TPSA 29.1 ✓ Ro5 ✓ Clean CC(C)(CCl)C(=O)Nc1ccc(cc1)C(F)(F)F
PHY RCSB PDB P07862 275.1 Da LogP 0.40 TPSA 147.2 ✓ Ro5 ✓ Clean C[C@@H](C[P@](=O)([C@@H](C)N)OP(=O)(O)O)C(=O)O
POB RCSB PDB P07862 291.1 Da LogP 0.47 TPSA 156.4 ✓ Ro5 ✓ Clean CC[C@H](C(=O)O)O[P@](=O)([C@@H](C)N)OP(=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.