KpKP13 Protein target profile

2-succinyl-6-hydroxy-2, 4-cyclohexadiene-1-carboxylate synthase

Accession: KP13_00976

Gene: menH AHE43494.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GW97
Export view
Length 252
Pocket druggability (P2Rank · AlphaFold DB model) 0.948
Direct ligand evidence 0 152 total records
Functional annotation 1 EC 2 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.

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.95, FPocket 0.73). Use the 3D pocket comparison to verify whether they identify the same site. Strong predicted binding pocket FPocket selected-pocket score 0.73. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.95. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Low human similarity A human hit was flagged, but identity is only 21.456% - a weak match, lower risk than a close homolog. This target also has a predicted binding pocket (P2Rank 0.95) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 75 of 4744 screened genomes (1.6%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.95) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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 (%)
21.456 Lower values reduce human off-target concern.
Human E-value
4.34e-08
Gut microbiome similarity
1.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
40.496 Higher values support similarity to known essential genes.
DEG E-value
8.98e-61 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.88 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) 0.948
Structure A0A0H3GW97
Pocket Pocket 1
Druggability (FPocket) 0.728
Structure A0A0H3GW97
Pocket Pocket 1
ColabFold model
P2Rank 0.953 · Pocket 1
FPocket 0.787 · Pocket 5
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 75 / 4744 genomes with a hit
Prevalence 1.6%

Sequence

Primary amino-acid sequence viewer.

MILSAAVDNGQPGYPWLVFLHGFSGDRNEWRKVGDAFPAWPRLYLDLPGHGGSADIAVQDFAGVNTLLQSTLNSYNIHKYWLIGYSLGGRVAMNFASQPRAGMRGLIVEGGHPGLQDVEARQARRSNDSAWAERFRREPLEQVFADWYQQPVFASLNAAQRESLVALRSRNNGATLAAMLQATSLAAQADLRASLQARDFPFHYLCGERDAKFRAIAQTLAADLHLIHHAGHNAHRDNPAAVIACLAQILAS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

2
  • GO:0009234 The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
  • GO:0070205 Catalysis of the reaction: 5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylate = (1R,6R)-2-succinyl-6-hydroxycyclohexa-2,4-diene-1-carboxylate + pyruvate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
17 243 Pfam PF12697 Alpha/beta hydrolase family
17 243 InterPro IPR000073 Alpha/beta hydrolase fold-1
15 250 NCBIfam TIGR03695 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
15 250 InterPro IPR022485 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
7 251 SUPERFAMILY SSF53474 alpha/beta-Hydrolases
7 251 InterPro IPR029058 Alpha/Beta hydrolase fold
15 251 PANTHER PTHR42916 2-SUCCINYL-5-ENOLPYRUVYL-6-HYDROXY-3-CYCLOHEXENE-1-CARBOXYLATE SYNTHASE
14 251 Hamap MF_01660 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase [menH].
14 251 InterPro IPR022485 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
1 250 Gene3D G3DSA:3.40.50.1820 alpha/beta hydrolase
1 250 InterPro IPR029058 Alpha/Beta hydrolase fold

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.948
Likely same site as FPocket 3 3.7 Å 16 shared residues 89% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.728
Show in viewer
Surrounding area
Pocket 2 FPocket #3
0.539
Likely same site as P2Rank 1 3.7 Å 16 shared residues 89% of smaller site
Show in viewer
Surrounding area
Pocket 3 FPocket #11
0.501
Show in viewer
Surrounding area
Pocket 4 FPocket #4
0.372
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_A0A0H3GW97
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_00976
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.

152 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 102 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
164 PDB via homolog 240.2 Da · LogP -0.02 · TPSA 111.9 Open detail RCSB PDB
PYR PDB via homolog Detail RCSB PDB
CHEMBL3263577 ChEMBL via homolog · pchembl 9.70 (~0.2 nM) Detail ChEMBL
CHEMBL3263579 ChEMBL via homolog · pchembl 9.70 (~0.2 nM) Detail ChEMBL
CHEMBL3263582 ChEMBL via homolog · pchembl 9.70 (~0.2 nM) Detail ChEMBL

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
164 RCSB PDB
4MYD
P37355 240.2 Da LogP -0.02 TPSA 111.9 ✓ Ro5 ✓ Clean C1=C[C@H]([C@@H](C(=C1)C(=O)CCC(=O)O)C(=O)O)O
PYR RCSB PDB
4MYS
P37355 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=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.

Cross-references

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

Sequence

UniProt A0A0H3GW97

Chemistry

ChEMBL CHEMBL3263577 ChEMBL CHEMBL3263579 ChEMBL CHEMBL3263582 ChEMBL CHEMBL5274434 ChEMBL CHEMBL3895863 ChEMBL CHEMBL3906477 ChEMBL CHEMBL4279328 ChEMBL CHEMBL4279884 ChEMBL CHEMBL4287766 ChEMBL CHEMBL4581240 ChEMBL CHEMBL4289572 ChEMBL CHEMBL4284689 ChEMBL CHEMBL3318603 ChEMBL CHEMBL3318604 ChEMBL CHEMBL3318612 ChEMBL CHEMBL4277989 ChEMBL CHEMBL4281842 ChEMBL CHEMBL4294845 ChEMBL CHEMBL3964338 ChEMBL CHEMBL3970032 ChEMBL CHEMBL4291201 ChEMBL CHEMBL4281906 ChEMBL CHEMBL2144065 ChEMBL CHEMBL3897587 ChEMBL CHEMBL3931744 ChEMBL CHEMBL3974512 ChEMBL CHEMBL3613671 ChEMBL CHEMBL5284566 ChEMBL CHEMBL3913807 ChEMBL CHEMBL606201 ChEMBL CHEMBL5740302 ChEMBL CHEMBL5743322 ChEMBL CHEMBL5753028 ChEMBL CHEMBL5756639 ChEMBL CHEMBL5758154 ChEMBL CHEMBL5768449 ChEMBL CHEMBL5772306 ChEMBL CHEMBL5782109 ChEMBL CHEMBL5788039 ChEMBL CHEMBL5821624 ChEMBL CHEMBL5825092 ChEMBL CHEMBL5832448 ChEMBL CHEMBL5851382 ChEMBL CHEMBL5855121 ChEMBL CHEMBL5859637 ChEMBL CHEMBL5860073 ChEMBL CHEMBL5864851 ChEMBL CHEMBL5874842 ChEMBL CHEMBL5893433 ChEMBL CHEMBL5901346 ChEMBL CHEMBL5913237 ChEMBL CHEMBL5937515 ChEMBL CHEMBL5945082 ChEMBL CHEMBL5949603 ChEMBL CHEMBL5950082 ChEMBL CHEMBL5962041 ChEMBL CHEMBL5962440 ChEMBL CHEMBL5965548 ChEMBL CHEMBL5983321 ChEMBL CHEMBL5985697 ChEMBL CHEMBL5996161 ChEMBL CHEMBL5998219 ChEMBL CHEMBL6009697 ChEMBL CHEMBL6015117 ChEMBL CHEMBL6022031 ChEMBL CHEMBL6029886 ChEMBL CHEMBL6035930 ChEMBL CHEMBL6040703 ChEMBL CHEMBL6052770 ChEMBL CHEMBL3318590 ChEMBL CHEMBL600429 ChEMBL CHEMBL4068554 ChEMBL CHEMBL4462665 ChEMBL CHEMBL4469632 ChEMBL CHEMBL4289712 ChEMBL CHEMBL4436074 ChEMBL CHEMBL3922787 ChEMBL CHEMBL3613161 ChEMBL CHEMBL3979183 ChEMBL CHEMBL591688 ChEMBL CHEMBL597515 ChEMBL CHEMBL3897762 ChEMBL CHEMBL3912754 ChEMBL CHEMBL3941507 ChEMBL CHEMBL4288486 ChEMBL CHEMBL3894067 ChEMBL CHEMBL599731 ChEMBL CHEMBL604948 ChEMBL CHEMBL3910417 ChEMBL CHEMBL4584757 ChEMBL CHEMBL3916842 ChEMBL CHEMBL3921538 ChEMBL CHEMBL3983619 ChEMBL CHEMBL3318611 ChEMBL CHEMBL601243 ChEMBL CHEMBL601244 ChEMBL CHEMBL3903742 ChEMBL CHEMBL3904310 ChEMBL CHEMBL3945728 ChEMBL CHEMBL4277826