Protein target profile

KP13_01723

Lysophospholipase L2

Genome: KpKP13 Gene: AHE46973.1 pldB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GGK6
Length 330
Pocket druggability 0.989
Direct ligand evidence 0 157 total records
Functional annotation 1 EC 3 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
2.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
96.15 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.989
Structure A0A0H3GGK6
Pocket Pocket 12
P2Rank 0.889
Structure A0A0H3GGK6
Pocket Pocket 1
ColabFold model
FPocket 0.652 · Pocket 9
P2Rank 0.753 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 101 / 4744 genomes with a hit
Prevalence 2.1%

Cross-references

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

Chemistry

ChEMBL CHEMBL5785193 ChEMBL CHEMBL5283351 ChEMBL CHEMBL5569248 ChEMBL CHEMBL5074982 ChEMBL CHEMBL5832941 ChEMBL CHEMBL4749516 ChEMBL CHEMBL5618354 ChEMBL CHEMBL5282368 ChEMBL CHEMBL5892322 ChEMBL CHEMBL4759880 ChEMBL CHEMBL4785835 ChEMBL CHEMBL5080928 ChEMBL CHEMBL5618586 ChEMBL CHEMBL5996643 ChEMBL CHEMBL5793684 ChEMBL CHEMBL5575673 ChEMBL CHEMBL5618723 ChEMBL CHEMBL5620200 ChEMBL CHEMBL5620312 ChEMBL CHEMBL4745872 ChEMBL CHEMBL5280083 ChEMBL CHEMBL5619084 ChEMBL CHEMBL5941658 ChEMBL CHEMBL3787346 ChEMBL CHEMBL5901923 ChEMBL CHEMBL5747079 ChEMBL CHEMBL6030416 ChEMBL CHEMBL5751521 ChEMBL CHEMBL5783701 ChEMBL CHEMBL4749293 ChEMBL CHEMBL4756662 ChEMBL CHEMBL5977282 ChEMBL CHEMBL5992406 ChEMBL CHEMBL6025412 ChEMBL CHEMBL5766234 ChEMBL CHEMBL5809976 ChEMBL CHEMBL6043445 ChEMBL CHEMBL5989783 ChEMBL CHEMBL6017690 ChEMBL CHEMBL4059676 ChEMBL CHEMBL4097203 ChEMBL CHEMBL5938868 ChEMBL CHEMBL6067709 ChEMBL CHEMBL3785379 ChEMBL CHEMBL5089721 ChEMBL CHEMBL5766195 ChEMBL CHEMBL5268216 ChEMBL CHEMBL6029674 ChEMBL CHEMBL5806570 ChEMBL CHEMBL5890841 ChEMBL CHEMBL5087880 ChEMBL CHEMBL5092936 ChEMBL CHEMBL5562095 ChEMBL CHEMBL5856728 ChEMBL CHEMBL5852867 ChEMBL CHEMBL5948496 ChEMBL CHEMBL5982150 ChEMBL CHEMBL6040834 ChEMBL CHEMBL5748180 ChEMBL CHEMBL5924021 ChEMBL CHEMBL5819297 ChEMBL CHEMBL5959609 ChEMBL CHEMBL4077745 ChEMBL CHEMBL5998656 ChEMBL CHEMBL6059594 ChEMBL CHEMBL5903041 ChEMBL CHEMBL5090735 ChEMBL CHEMBL6061710 ChEMBL CHEMBL3087181 ChEMBL CHEMBL5073483 ChEMBL CHEMBL4875383 ChEMBL CHEMBL6034498 ChEMBL CHEMBL4078217 ChEMBL CHEMBL5807603 ChEMBL CHEMBL5971486 ChEMBL CHEMBL5974214 ChEMBL CHEMBL5897972 ChEMBL CHEMBL5953601 ChEMBL CHEMBL5759972 ChEMBL CHEMBL5869514 ChEMBL CHEMBL5423658 ChEMBL CHEMBL5563952 ChEMBL CHEMBL5567001 ChEMBL CHEMBL5075857 ChEMBL CHEMBL5910702 ChEMBL CHEMBL5929810 ChEMBL CHEMBL2159781 ChEMBL CHEMBL5861814 ChEMBL CHEMBL5867880 ChEMBL CHEMBL3356971 ChEMBL CHEMBL4216513 ChEMBL CHEMBL6046506 ChEMBL CHEMBL5781750 ChEMBL CHEMBL6036379 ChEMBL CHEMBL5813078 ChEMBL CHEMBL4204645 ChEMBL CHEMBL5561265 ChEMBL CHEMBL5765531 ChEMBL CHEMBL5930021 ChEMBL CHEMBL6061587

Sequence

Primary amino-acid sequence viewer.

MFGQKKDWETRENAFAAFSMGPLTDFWRQREEAEFKGVDDVPVRFVRFCAQHNDRLVLICPGRIESYVKYAEVAYDLFHCGFDVMIIDHRGQGRSGRLLSDTHRGHVVNFSDYVDDLAALWQQQVVPGHWRKRFILAHSMGGAIATLFLQRYRAHCDAIALCAPMFGIIIRLPDWMVRHILDWAEGHQRIREEYAIGTGRWRALPFAVNVLTHSRQRYRRNLRFYADEPRLQVGGPTWHWVREGMLAGDEVLANVEKDTAPTLLLQAEEERVVDNLMHDRYCELRAAAGHPCEGGKPLVIEGAYHEILFEKDAMRSVALNAIVEFFNRHT

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0004622 Catalysis of the reaction: a 1-acyl-sn-glycero-3-phosphocholine + H2O = a fatty acid + H+ + sn-glycerol 3-phosphocholine.
  • GO:0006629 The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

8 records
Show feature table
Start End DB Term Name
25 330 Gene3D G3DSA:3.40.50.1820 alpha/beta hydrolase
25 330 InterPro IPR029058 Alpha/Beta hydrolase fold
17 329 SUPERFAMILY SSF53474 alpha/beta-Hydrolases
17 329 InterPro IPR029058 Alpha/Beta hydrolase fold
52 312 Pfam PF12146 Serine aminopeptidase, S33
52 312 InterPro IPR022742 Serine aminopeptidase, S33
55 328 PANTHER PTHR11614 PHOSPHOLIPASE-RELATED
24 330 FunFam G3DSA:3.40.50.1820:FF:000020 Lysophospholipase L2

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 · FPocket

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

Site 1 FPocket #12
0.989
Likely same site as P2Rank 1 5.5 Å 28 shared residues 88% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.889
Likely same site as FPocket 12 5.5 Å 28 shared residues 88% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.275
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.115
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.039
Show in viewer
Surrounding area
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_A0A0H3GGK6
AlphaFold DB full sequence Viewing
ColabFold KP13_01723
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.

157 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 107 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
9JX PDB via homolog 467.0 Da · LogP 4.03 · TPSA 56.8 Open detail RCSB PDB
C0S PDB via homolog Detail RCSB PDB
E3A PDB via homolog Detail RCSB PDB
F4P PDB via homolog Detail RCSB PDB
XOV 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
9JX RCSB PDB Q99685 467.0 Da LogP 4.03 TPSA 56.8 ✓ Ro5 ✓ Clean c1ccc(c(c1)c2cccc(c2)N3C[C@@H](CC3=O)N4CCN(CC4)…
C0S RCSB PDB Q99685 395.3 Da LogP 3.77 TPSA 68.5 ✓ Ro5 ✓ Clean c1ccc(cc1)c2nc(on2)C3CN(C3)C(=O)OC(C(F)(F)F)C(F…
E3A RCSB PDB Q99685 384.4 Da LogP 1.86 TPSA 84.7 ✓ Ro5 ✓ Clean c1cc(ccc1n2ccc(n2)C3[C@H]4[C@@H]3CN(C4)C(=O)ON5…
F4P RCSB PDB Q99685 383.4 Da LogP 2.93 TPSA 54.3 ✓ Ro5 ✓ Clean c1cc(ccc1C(c2ccc(cc2)F)N3CCN(CC3)C(=O)n4cncn4)F
XOV RCSB PDB Q99685 396.8 Da LogP 2.99 TPSA 67.9 ✓ Ro5 ✓ Clean c1cc(c(cc1F)Cl)OCC2CCN(CC2)C(=O)C3CC4(C3)COC(=O…
XP7 RCSB PDB Q99685 382.9 Da LogP 3.16 TPSA 58.6 ✓ Ro5 ✓ Clean c1cc(c(cc1F)Cl)OCC2CCN(CC2)C(=O)CC[C@@H]3CCC(=O…
XPD RCSB PDB Q99685 418.9 Da LogP 3.74 TPSA 67.9 ✓ Ro5 ✓ Clean c1cc2c(cc1C(=O)N3CCC(CC3)COc4ccc(cc4Cl)F)NC(=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.