Protein target profile

KP13_04751

Adenosylhomocysteinase

Genome: KpKP13 Gene: AHE43714.1 ahcY 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQL2
Length 369
Pocket druggability 0.648
Direct ligand evidence 0 157 total records
Functional annotation 0 EC 4 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
Hit
Human identity (%)
32.979 Lower values reduce human off-target concern.
Human E-value
6.62e-40
Gut microbiome similarity
0.3% 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
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.64 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 0.648
Structure A0A0H3GQL2
Pocket Pocket 2
P2Rank 0.962
Structure A0A0H3GQL2
Pocket Pocket 1
ColabFold model
FPocket 0.809 · Pocket 1
P2Rank 0.968 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 15 / 4744 genomes with a hit
Prevalence 0.3%

Cross-references

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

Chemistry

ChEMBL CHEMBL154745 ChEMBL CHEMBL280595 ChEMBL CHEMBL3290657 ChEMBL 6OS ChEMBL CHEMBL301499 ChEMBL CHEMBL3322562 ChEMBL CHEMBL3290658 ChEMBL CHEMBL2059155 ChEMBL CHEMBL3290668 ChEMBL CHEMBL3753637 ChEMBL CHEMBL281476 ChEMBL CHEMBL268272 ChEMBL CHEMBL2115462 ChEMBL CHEMBL3597832 ChEMBL CHEMBL3290663 ChEMBL CHEMBL3322547 ChEMBL CHEMBL3753746 ChEMBL CHEMBL281337 ChEMBL CHEMBL50728 ChEMBL CHEMBL50306 ChEMBL CHEMBL3290665 ChEMBL CHEMBL284846 ChEMBL CHEMBL147260 ChEMBL CHEMBL3290659 ChEMBL CHEMBL308037 ChEMBL CHEMBL77518 ChEMBL CHEMBL2374428 ChEMBL CHEMBL299961 ChEMBL CHEMBL3290662 ChEMBL CHEMBL3322550 ChEMBL CHEMBL3322549 ChEMBL CHEMBL3322556 ChEMBL CHEMBL3597818 ChEMBL CHEMBL3322540 ChEMBL CHEMBL3322555 ChEMBL CHEMBL3597817 ChEMBL CHEMBL3322554 ChEMBL CHEMBL3597816 ChEMBL CHEMBL53931 ChEMBL CHEMBL3322541 ChEMBL CHEMBL296880 ChEMBL CHEMBL606276 ChEMBL CHEMBL608056 ChEMBL CHEMBL3290655 ChEMBL CHEMBL605902 ChEMBL 7CY ChEMBL CHEMBL2092790 ChEMBL CHEMBL3322559 ChEMBL CHEMBL3597821 ChEMBL CHEMBL49908 ChEMBL CHEMBL605900 ChEMBL CHEMBL45537 ChEMBL CHEMBL3322553 ChEMBL CHEMBL2092789 ChEMBL CHEMBL3322561 ChEMBL CHEMBL3597823 ChEMBL CHEMBL49511 ChEMBL NRN ChEMBL CHEMBL50600 ChEMBL CHEMBL415930 ChEMBL CHEMBL2115031 ChEMBL CHEMBL3290660 ChEMBL CHEMBL419393 ChEMBL CHEMBL3322548 ChEMBL CHEMBL416457 ChEMBL CHEMBL49737 ChEMBL CHEMBL3349025 ChEMBL CHEMBL3322545 ChEMBL CHEMBL64718 ChEMBL CHEMBL77965 ChEMBL CHEMBL494759 ChEMBL CHEMBL3322552 ChEMBL CHEMBL610148 ChEMBL CHEMBL3322551 ChEMBL CHEMBL49917 ChEMBL CHEMBL3322534 ChEMBL CHEMBL4638533 ChEMBL CHEMBL612224 ChEMBL CHEMBL4635734 ChEMBL CHEMBL3322533 ChEMBL CHEMBL1098945 ChEMBL CHEMBL595547 ChEMBL CHEMBL310547 ChEMBL CHEMBL295729 ChEMBL CHEMBL3322532 ChEMBL CHEMBL3322542 ChEMBL CHEMBL611098 ChEMBL CHEMBL608072 ChEMBL CHEMBL610383 ChEMBL CHEMBL296392 ChEMBL CHEMBL3322560 ChEMBL CHEMBL3597822 ChEMBL CHEMBL3597813 ChEMBL CHEMBL1288616 ChEMBL CHEMBL2364569 ChEMBL CHEMBL3290661 ChEMBL CHEMBL604208 ChEMBL CHEMBL610384 ChEMBL CHEMBL4538845 ChEMBL CHEMBL608915

Sequence

Primary amino-acid sequence viewer.

MNNKISLAKEVAWASQNMPRTLRQVAALPDLSGVRLACCMHLDMKMIPLVQGILDKGAQVFLTTCNPTTVQDDVVAWLVERGAEACAWRNMSDADWQQSWEKAIAWQPTHLCEMGADITTLLHQRGEFGNIVAGLEATGSGVNRLGDIQPGYPIFNWDDLPVKEGLHNRHMVGLTAWHTFFQTTHLTLHEKKVLVIGYGLVGQGVAAAAKAFGGQVMVAEIDPARRLQAAYDGWHVVDLQEAIASADVVATATGGKNVVNRQALDRTKAGVFILNVGHVAEEIDGDYLRQYPQEEVMPYINAYRMADKTVYLLANGSMLNLTAGFGDSLNAFDVTLAVMASGIRHIVTEGMRAPAKVYLLPQAVWQQAL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004013 Catalysis of the reaction: S-adenosyl-L-homocysteine + H2O = adenosine + L-homocysteine.
  • GO:0006730 The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
  • GO:0033353 A cyclic series of interconversions involving S-adenosyl-L-homocysteine, L-homocysteine, L-methionine and S-adenosyl-L-methionine (SAM). Couples utilization of the methyl group of SAM with recycling of the homocysteinyl group and regeneration of L-methionine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
9 364 Gene3D G3DSA:3.40.50.1480 -
9 364 InterPro IPR042172 Adenosylhomocysteinase-like superfamily
168 326 SMART SM00997 AdoHcyase_NAD_2
168 326 InterPro IPR015878 S-adenosyl-L-homocysteine hydrolase, NAD binding domain
9 127 Pfam PF05221 S-adenosyl-L-homocysteine hydrolase
9 127 InterPro IPR000043 Adenosylhomocysteinase-like
170 325 Gene3D G3DSA:3.40.50.720 -
168 326 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
168 326 InterPro IPR036291 NAD(P)-binding domain superfamily
9 364 PANTHER PTHR23420 ADENOSYLHOMOCYSTEINASE
9 364 InterPro IPR000043 Adenosylhomocysteinase-like
182 323 Pfam PF00670 S-adenosyl-L-homocysteine hydrolase, NAD binding domain
182 323 InterPro IPR015878 S-adenosyl-L-homocysteine hydrolase, NAD binding domain
9 364 SUPERFAMILY SSF52283 Formate/glycerate dehydrogenase catalytic domain-like
3 368 SMART SM00996 AdoHcyase_2
3 368 InterPro IPR000043 Adenosylhomocysteinase-like

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 #2
0.648
Likely same site as P2Rank 1 2.1 Å 31 shared residues 94% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #1
0.464
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
0.962
Likely same site as FPocket 2 2.1 Å 31 shared residues 94% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.513
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.015
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_A0A0H3GQL2
AlphaFold DB full sequence Viewing
ColabFold KP13_04751
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
9W1 PDB via homolog 394.4 Da · LogP 2.74 · TPSA 119.4 Open detail RCSB PDB
9W4 PDB via homolog Detail RCSB PDB
ADC PDB via homolog Detail RCSB PDB
ADN PDB via homolog Detail RCSB PDB
AFX 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
9W1 RCSB PDB P23526 394.4 Da LogP 2.74 TPSA 119.4 ✓ Ro5 ✓ Clean Cc1cc(cc(n1)[C@@H]2CCN(C2)C(=O)c3c(non3)N)Nc4cc…
9W4 RCSB PDB P23526 449.5 Da LogP 2.92 TPSA 104.2 ✓ Ro5 ✓ Clean c1cc(ccc1CN2C(=O)C=NC2=O)C(=O)Nc3ccc4c(c3)sc(n4…
ADC RCSB PDB P23526 233.2 Da LogP -0.76 TPSA 110.1 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@@H]3C=CC([C@H]3O)O)N
ADN RCSB PDB A0A077EDS4 267.2 Da LogP -1.98 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AFX RCSB PDB P23526 279.2 Da LogP -0.89 TPSA 127.2 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H](C(=O)C(=C3F)CO)O…
NOC RCSB PDB P23526 265.3 Da LogP -1.32 TPSA 130.3 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@@H]3CC([C@@H]([C@H]3O)O)CO…
XFA RCSB PDB P23526 556.5 Da LogP 4.32 TPSA 77.1 1 viol. ✓ Clean CNCCNC(=O)CN(CC(=O)N(C)N1Cc2ccccc2C1)c3cc(ccc3O…

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.