Protein target profile

KP13_00707

Ribulose-phosphate 3-epimerase

Genome: KpKP13 Gene: rpe AHE42325.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GYE8

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Length 227

Pocket druggability 0.267

Direct ligand evidence 0 55 total records

Functional annotation 1 EC 7 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 (%): 39.459 Lower values reduce human off-target concern.
Human E-value: 1.96e-39
Gut microbiome similarity: 13.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 94.643 Higher values support similarity to known essential genes.
DEG E-value: 3.03e-158 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 96.76 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 0.267

Structure A0A0H3GYE8

Pocket Pocket 3

P2Rank 0.819

Structure A0A0H3GYE8

Pocket Pocket 1

ColabFold model

FPocket 0.076 · Pocket 11

P2Rank 0.833 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 661 / 4744 genomes with a hit

Prevalence 13.9%

Cross-references

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

Sequence

UniProt A0A0H3GYE8

Sequence

Primary amino-acid sequence viewer.

MRMKQYLIAPSILSADFARLGEDTAKALAAGADVVHFDVMDNHYVPNLTIGPMVLKSLRNYGITAPIDVHLMVKPVDRIIPDFAEAGASIITFHPEASEHVDRSLQLIKEHGCKAGLVFNPATPLSYLDYVMDKLDVILLMSVNPGFGGQSFIPQTLDKLREVRQRIDASGYDIRLEVDGGVKASNIGEIAAAGADMFVAGSAIFGQPDYKQVIDQMRSELAKVSHG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

5.1.3.1

Gene Ontology (GO)

GO:0004750 Catalysis of the reaction: D-ribulose 5-phosphate = D-xylulose 5-phosphate.
GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
GO:0016857 Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule.
GO:0006098 The metabolic process in which glucose-6-phosphate is oxidized to form carbon dioxide (CO2) and ribulose 5-phosphate, coupled to reduction of NADP+ to NADPH; ribulose 5-P then enters a series of reactions that can yield biosynthetic precursors (ribose-5-phosphate and erythrose-4-phosphate) and glycolytic intermediates (fructose-6-phosphate and glyceraldehyde-3-phosphate).
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0046872 Binding to a metal ion.
GO:0019323 The chemical reactions and pathways resulting in the breakdown of a pentose, any monosaccharide with a chain of five carbon atoms in the molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
35	49	ProSitePatterns	PS01085	Ribulose-phosphate 3-epimerase family signature 1.
35	49	InterPro	IPR000056	Ribulose-phosphate 3-epimerase-like
2	221	SUPERFAMILY	SSF51366	Ribulose-phoshate binding barrel
2	221	InterPro	IPR011060	Ribulose-phosphate binding barrel
1	225	Gene3D	G3DSA:3.20.20.70	Aldolase class I
1	225	InterPro	IPR013785	Aldolase-type TIM barrel
2	227	PIRSF	PIRSF001461	RPE
2	227	InterPro	IPR026019	Ribulose-phosphate 3-epimerase
5	220	Hamap	MF_02227	Ribulose-phosphate 3-epimerase [rpe].
5	220	InterPro	IPR026019	Ribulose-phosphate 3-epimerase
7	218	CDD	cd00429	RPE
7	218	InterPro	IPR000056	Ribulose-phosphate 3-epimerase-like
7	223	PANTHER	PTHR11749	RIBULOSE-5-PHOSPHATE-3-EPIMERASE
7	223	InterPro	IPR000056	Ribulose-phosphate 3-epimerase-like
8	205	Pfam	PF00834	Ribulose-phosphate 3 epimerase family
8	205	InterPro	IPR000056	Ribulose-phosphate 3-epimerase-like
138	160	ProSitePatterns	PS01086	Ribulose-phosphate 3-epimerase family signature 2.
138	160	InterPro	IPR000056	Ribulose-phosphate 3-epimerase-like
7	218	NCBIfam	TIGR01163	ribulose-phosphate 3-epimerase
7	218	InterPro	IPR026019	Ribulose-phosphate 3-epimerase
3	224	FunFam	G3DSA:3.20.20.70:FF:000004	Ribulose-phosphate 3-epimerase

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 #3

0.267

Likely same site as P2Rank 2 1.6 Å 11 shared residues 100% of smaller site

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Surrounding area

Site 2 FPocket #2

0.209

Likely same site as P2Rank 3 2.9 Å 8 shared residues 100% of smaller site

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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.819

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Surrounding area

Site 2 P2Rank #2

0.038

Likely same site as FPocket 3 1.6 Å 11 shared residues 100% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.011

Likely same site as FPocket 2 2.9 Å 8 shared residues 100% of smaller site

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Surrounding area

Residue sets

UniProt: Active site:177-177 Proton donor

UniProt: Active site:36-36 Proton acceptor

UniProt: Binding site:144-147

UniProt: Binding site:177-177

UniProt: Binding site:177-179

UniProt: Binding site:179-179

UniProt: Binding site:199-200

UniProt: Binding site:34-34

UniProt: Binding site:36-36

UniProt: Binding site:68-68

UniProt: Binding site:9-9

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.833

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Surrounding area

Site 2 P2Rank #2

0.134

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Surrounding area

Site 3 P2Rank #3

0.032

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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_A0A0H3GYE8	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_00707	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

5RP PDB via homolog 230.1 Da · LogP -2.62 · TPSA 144.5 Open detail RCSB PDB

5SP PDB via homolog Detail RCSB PDB

DX5 PDB via homolog Detail RCSB PDB

S6P PDB via homolog Detail RCSB PDB

XPE PDB via homolog Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
5RP RCSB PDB	3OVQ	Q96AT9	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`C([C@H]([C@H](C(=O)CO)O)O)OP(=O)(O)O`
5SP RCSB PDB	3OVR	Q96AT9	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`C([C@H]([C@@H](C(=O)CO)O)O)OP(=O)(O)O`
DX5 RCSB PDB	2FLI	Q9A1H8	232.1 Da LogP -2.83 TPSA 147.7	1 viol.	✓ Clean	`C([C@@H]([C@H]([C@@H](COP(=O)(O)O)O)O)O)O`
S6P RCSB PDB	3CTL	P32719	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`C([C@@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)…`
XPE RCSB PDB	3OVP	Q96AT9	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`C(COCCOCCOCCOCCOCCOCCOCCOCCOCCO)O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC12501520 ZINC	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC2522704 ZINC	1.000	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC3874716 ZINC	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769 ZINC	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548 ZINC	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829 ZINC	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830 ZINC	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC2516111 ZINC	0.917	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC3869812 ZINC	0.917	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC5975509 ZINC	0.760	202.1 Da LogP -2.19 TPSA 127.5	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)CO`
ZINC115086873 ZINC	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264 ZINC	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823 ZINC	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442 ZINC	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710 ZINC	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161 ZINC	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118 ZINC	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257 ZINC	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028 ZINC	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057 ZINC	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776 ZINC	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654 ZINC	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157 ZINC	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059 ZINC	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101 ZINC	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743 ZINC	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860 ZINC	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917 ZINC	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182 ZINC	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921 ZINC	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446 ZINC	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447 ZINC	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC144169243 ZINC	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716 ZINC	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC575441396 ZINC	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC25721582 ZINC	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC25721586 ZINC	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC4544030 ZINC	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4544032 ZINC	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4544034 ZINC	0.633	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887586 ZINC	0.633	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887587 ZINC	0.633	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887588 ZINC	0.633	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4887589 ZINC	0.633	260.1 Da LogP -2.35 TPSA 164.8	1 viol.	✓ Clean	`O=C(O)C[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC100065511 ZINC	0.613	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC100085043 ZINC	0.613	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC104869937 ZINC	0.613	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC13537943 ZINC	0.613	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC85994845 ZINC	0.613	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1644613 ZINC	0.611	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`

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.

KP13_00707

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

Main supporting evidence

Risks to review

Evidence gaps

Prioritization evidence

Off-target risk

Essentiality

Localization

Structure confidence

Binding-site evidence

Cross-references

Sequence

Sequence

Functional annotations

Enzyme Commission (EC)

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · FPocket

Binding pockets · P2Rank

Binding pockets · P2Rank

Structural evidence

Ligand evidence