Protein target profile

KP13_02726

S-adenosylmethionine synthase

Genome: KpKP13 Gene: metK AHE42706.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GXI4
Length 384
Pocket druggability 0.387
Direct ligand evidence 0 170 total records
Functional annotation 1 EC 6 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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 (%)
58.221 Lower values reduce human off-target concern.
Human E-value
3.0000000000000004e-144
Gut microbiome similarity
70.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.61 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 0.387
Structure A0A0H3GXI4
Pocket Pocket 1
P2Rank 0.272
Structure A0A0H3GXI4
Pocket Pocket 1
ColabFold model
FPocket 0.173 · Pocket 4
P2Rank 0.132 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3337 / 4744 genomes with a hit
Prevalence 70.3%

Cross-references

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

Chemistry

ChEMBL WBG ChEMBL CHEMBL4521249 ChEMBL CHEMBL4552959 ChEMBL CHEMBL4558617 ChEMBL CHEMBL4568226 ChEMBL CHEMBL4582312 ChEMBL WBS ChEMBL CHEMBL4860456 ChEMBL CHEMBL4870597 ChEMBL CHEMBL4585665 ChEMBL CHEMBL4584451 ChEMBL TQB ChEMBL CHEMBL4559088 ChEMBL CHEMBL5078281 ChEMBL CHEMBL5557849 ChEMBL CHEMBL5085027 ChEMBL CHEMBL5560825 ChEMBL TO5 ChEMBL CHEMBL5559663 ChEMBL CHEMBL5565126 ChEMBL CHEMBL4590059 ChEMBL CHEMBL5560183 ChEMBL CHEMBL4529030 ChEMBL CHEMBL5568212 ChEMBL CHEMBL5566494 ChEMBL CHEMBL4587880 ChEMBL CHEMBL5563344 ChEMBL CHEMBL5427280 ChEMBL CHEMBL5560026 ChEMBL CHEMBL5563550 ChEMBL CHEMBL5561357 ChEMBL CHEMBL5556562 ChEMBL CHEMBL5557591 ChEMBL CHEMBL4549681 ChEMBL CHEMBL5532050 ChEMBL CHEMBL4483464 ChEMBL J4A ChEMBL CHEMBL5523372 ChEMBL CHEMBL5555870 ChEMBL CHEMBL4561247 ChEMBL CHEMBL5561963 ChEMBL CHEMBL4582351 ChEMBL CHEMBL5561779 ChEMBL CHEMBL5560624 ChEMBL CHEMBL4552037 ChEMBL CHEMBL4483341 ChEMBL CHEMBL4514719 ChEMBL CHEMBL4516541 ChEMBL CHEMBL4521225 ChEMBL CHEMBL4522257 ChEMBL CHEMBL4522713 ChEMBL CHEMBL4525301 ChEMBL CHEMBL4527123 ChEMBL CHEMBL4527921 ChEMBL CHEMBL4530602 ChEMBL CHEMBL4538283 ChEMBL CHEMBL4542083 ChEMBL CHEMBL4546271 ChEMBL CHEMBL4546633 ChEMBL CHEMBL4546944 ChEMBL CHEMBL4551093 ChEMBL CHEMBL4553872 ChEMBL CHEMBL4555060 ChEMBL CHEMBL4558233 ChEMBL CHEMBL4561105 ChEMBL CHEMBL4561650 ChEMBL CHEMBL4562374 ChEMBL CHEMBL4567243 ChEMBL CHEMBL4567650 ChEMBL CHEMBL4568510 ChEMBL CHEMBL4568635 ChEMBL CHEMBL4569602 ChEMBL CHEMBL4571843 ChEMBL CHEMBL4572719 ChEMBL CHEMBL4573526 ChEMBL CHEMBL4573728 ChEMBL CHEMBL4576190 ChEMBL CHEMBL4578643 ChEMBL CHEMBL4580282 ChEMBL CHEMBL4583730 ChEMBL CHEMBL4588181 ChEMBL CHEMBL4856769 ChEMBL CHEMBL3706401 ChEMBL CHEMBL5561633 ChEMBL CHEMBL3706402 ChEMBL CHEMBL4531472 ChEMBL CHEMBL4551583 ChEMBL CHEMBL4865263 ChEMBL CHEMBL4877839 ChEMBL WBM ChEMBL CHEMBL5757695 ChEMBL CHEMBL5772510 ChEMBL CHEMBL5774989 ChEMBL CHEMBL5775639 ChEMBL CHEMBL5778586 ChEMBL CHEMBL5784458 ChEMBL CHEMBL5787367 ChEMBL CHEMBL5823027 ChEMBL CHEMBL5828518 ChEMBL CHEMBL5863551

Sequence

Primary amino-acid sequence viewer.

MAKHLFTSESVSEGHPDKIADQISDAVLDAILEQDPKARVACETYVKTGMVLVGGEITTSAWVDIEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQSPDINQGVDRADPLEQGAGDQGLMFGYATNETDVLMPAPVTYAHRLVQRQAEVRKNGTLPWLRPDAKSQVTFQYDDGKIVGIDAVVLSTQHAEDIDQKSLQEAVMEEIIKPILPTEWLNASTKFFINPTGRFVIGGPMGDCGLTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSAAYAARYVAKNIVAAGLADRCEIQVSYAIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFDLRPYGLIQMLDLLHPIYKETAAYGHFGREHFPWEKTDKAALLREAAGLK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0006556 The chemical reactions and pathways resulting in the formation of S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
  • GO:0004478 Catalysis of the reaction: ATP + L-methionine + H2O = phosphate + diphosphate + S-adenosyl-L-methionine.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0006730 The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
3 377 PANTHER PTHR11964 S-ADENOSYLMETHIONINE SYNTHETASE
3 377 InterPro IPR002133 S-adenosylmethionine synthetase
11 270 Gene3D G3DSA:3.30.300.10 -
5 233 Gene3D G3DSA:3.30.300.10 -
233 370 Pfam PF02773 S-adenosylmethionine synthetase, C-terminal domain
233 370 InterPro IPR022630 S-adenosylmethionine synthetase, C-terminal
112 232 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase
112 232 InterPro IPR022636 S-adenosylmethionine synthetase superfamily
5 372 CDD cd18079 S-AdoMet_synt
11 126 FunFam G3DSA:3.30.300.10:FF:000001 S-adenosylmethionine synthase
5 380 NCBIfam TIGR01034 methionine adenosyltransferase
5 380 InterPro IPR002133 S-adenosylmethionine synthetase
2 381 Hamap MF_00086 S-adenosylmethionine synthase [metK].
2 381 InterPro IPR002133 S-adenosylmethionine synthetase
259 267 ProSitePatterns PS00377 S-adenosylmethionine synthase signature 2.
259 267 InterPro IPR022631 S-adenosylmethionine synthetase, conserved site
103 374 Gene3D G3DSA:3.30.300.10 -
233 382 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase
233 382 InterPro IPR022636 S-adenosylmethionine synthetase superfamily
114 231 Pfam PF02772 S-adenosylmethionine synthetase, central domain
114 231 InterPro IPR022629 S-adenosylmethionine synthetase, central domain
135 234 FunFam G3DSA:3.30.300.10:FF:000003 S-adenosylmethionine synthase
116 126 ProSitePatterns PS00376 S-adenosylmethionine synthase signature 1.
116 126 InterPro IPR022631 S-adenosylmethionine synthetase, conserved site
4 101 Pfam PF00438 S-adenosylmethionine synthetase, N-terminal domain
4 101 InterPro IPR022628 S-adenosylmethionine synthetase, N-terminal
1 382 PIRSF PIRSF000497 MAT
1 382 InterPro IPR002133 S-adenosylmethionine synthetase
3 109 SUPERFAMILY SSF55973 S-adenosylmethionine synthetase
3 109 InterPro IPR022636 S-adenosylmethionine synthetase superfamily

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 #1
0.387
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #12
0.248
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.272
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.046
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.029
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.018
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.009
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:15-15 in other chain
UniProt: Binding site:164-166 in other chain
UniProt: Binding site:17-17
UniProt: Binding site:230-231 in other chain
UniProt: Binding site:239-239
UniProt: Binding site:245-246 in other chain
UniProt: Binding site:262-262
UniProt: Binding site:266-266
UniProt: Binding site:270-270 in other chain
UniProt: Binding site:43-43
UniProt: Binding site:56-56 in other chain
UniProt: Binding site:99-99 in other chain
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_A0A0H3GXI4
AlphaFold DB full sequence Viewing
ColabFold KP13_02726
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.

170 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 120 records from similar proteins
Structural ligands 20 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3PO PDB via homolog 258.0 Da · LogP -0.69 · TPSA 170.8 Open detail RCSB PDB
ABP PDB via homolog Detail RCSB PDB
ADN PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
APC 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
3PO RCSB PDB Q5FAC0 258.0 Da LogP -0.69 TPSA 170.8 ✓ Ro5 ✓ Clean OP(=O)(O)OP(=O)(O)OP(=O)(O)O
ABP RCSB PDB P0A817 506.1 Da LogP -0.98 TPSA 232.6 3 viol. ✓ Clean c1nc(c2c(n1)n(c(n2)Br)[C@H]3[C@@H]([C@@H]([C@H]…
ADN RCSB PDB P31153 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)…
ANP RCSB PDB P0A817 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)…
APC RCSB PDB P17562 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
J41 RCSB PDB P31153 301.3 Da LogP 3.67 TPSA 50.2 ✓ Ro5 ✓ Clean CC1=CC(=O)n2c(c(c(n2)c3ccccc3)c4ccccc4)N1
MED RCSB PDB P31153 149.2 Da LogP 0.15 TPSA 63.3 ✓ Ro5 ✓ Clean CSCC[C@H](C(=O)O)N
MXE RCSB PDB P17562 76.1 Da LogP -0.37 TPSA 29.5 ✓ Ro5 ✓ Clean COCCO
PE8 RCSB PDB P17562 370.4 Da LogP -0.91 TPSA 105.1 ✓ Ro5 ✓ Clean C(COCCOCCOCCOCCOCCOCCOCCO)O
POP RCSB PDB P0A817 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
PPK RCSB PDB P0A817 257.0 Da LogP -1.12 TPSA 173.6 1 viol. ✓ Clean N(P(=O)(O)O)[P@](=O)(O)OP(=O)(O)O
PPV RCSB PDB P31153 178.0 Da LogP -0.81 TPSA 124.3 ✓ Ro5 ✓ Clean OP(=O)(O)OP(=O)(O)O
S7M RCSB PDB P31153 413.5 Da LogP -1.53 TPSA 182.6 ✓ Ro5 ✓ Clean CC[S+](CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C…
TNW RCSB PDB P31153 313.8 Da LogP 3.41 TPSA 38.1 ✓ Ro5 ✓ Clean Cc1cccc(c1)N2c3cc(ccc3C(=NC2=O)N(C)C)Cl
TNZ RCSB PDB P31153 270.7 Da LogP 3.96 TPSA 35.0 ✓ Ro5 ✓ Clean COc1nc2ccc(cc2c(n1)c3ccccc3)Cl
TO8 RCSB PDB P31153 223.7 Da LogP 1.64 TPSA 49.0 ✓ Ro5 ✓ Clean CN(C)C1=NC(=O)Nc2c1ccc(c2)Cl
TOW RCSB PDB P31153 267.7 Da LogP 1.11 TPSA 58.4 ✓ Ro5 ✓ Clean CN(C)C1=NC(=O)N(c2c1ccc(c2)Cl)CCO
TQE RCSB PDB P31153 184.2 Da LogP -0.37 TPSA 71.1 ✓ Ro5 ✓ Clean CCOC1=NC(=NC(=O)N1)N(C)C
U4P RCSB PDB P31153 228.2 Da LogP -1.82 TPSA 104.6 ✓ Ro5 ✓ Clean C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)O…
YQP RCSB PDB P31153 375.4 Da LogP -2.34 TPSA 167.9 ✓ Ro5 ✓ Clean C=S(CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H…

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.