Protein target profile

HT085_RS00085

triose-phosphate isomerase

Genome: NZ_AP023069.1 Gene: WHOF_00409 N776_09260 TUM19854C_00130 WHOF_00015C NGO_0017 tpiA ESCNG_30034 3D evidence: AlphaFold DB model UniProt A0AA44U8M8 UniProt Q5FAJ7 UniProt A0AB74ER61

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Length 257

Direct ligand evidence 0 60 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
Gut microbiome off-target: Hit

Essentiality

Essential (DEG): Y

Localization

Localization: Cytoplasmic

Binding-site evidence

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 High

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MYRQIGMWDQKWVIGNWKMNGRLQNNNALMHRFRILPTAERVLIGLAAPTVYLLQLHNAMQIVLNNRILTCAQDVSRFPDNGAYTGEVSAEMLADTGTDIVLIGHSERSLYFGEKNEIQRRKMENVLNVGLIPLLCVGESLEERETGKEHEVIAHQLSILQGLDTKNIAVAYEPVWAIGTGKVATVEQIADMHAFIYKEILSLCGSDVKIRVLYGGSVKADNAADIFAVPYVDGALVGGASLSYDSFTAIISAAQNA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

5.3.1.1

Gene Ontology (GO)

GO:0006096 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
GO:0004807 Catalysis of the reaction: D-glyceraldehyde 3-phosphate = dihydroxyacetone phosphate.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0006094 The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
GO:0046166 The chemical reactions and pathways resulting in the formation of glyceraldehyde-3-phosphate, an important intermediate in glycolysis.
GO:0019563 The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
11	253	Pfam	PF00121	Triosephosphate isomerase
11	253	InterPro	IPR000652	Triosephosphate isomerase
8	254	SUPERFAMILY	SSF51351	Triosephosphate isomerase (TIM)
8	254	InterPro	IPR035990	Triosephosphate isomerase superfamily
11	252	CDD	cd00311	TIM
11	252	InterPro	IPR000652	Triosephosphate isomerase
9	253	Hamap	MF_00147_B	Triosephosphate isomerase [tpiA].
9	253	InterPro	IPR022896	Triosephosphate isomerase, bacterial/eukaryotic
3	257	Gene3D	G3DSA:3.20.20.70	Aldolase class I
3	257	InterPro	IPR013785	Aldolase-type TIM barrel
10	252	PANTHER	PTHR21139	TRIOSEPHOSPHATE ISOMERASE
10	252	InterPro	IPR000652	Triosephosphate isomerase
10	253	ProSiteProfiles	PS51440	Triosephosphate isomerase (TIM) family profile.
10	253	InterPro	IPR000652	Triosephosphate isomerase
171	181	ProSitePatterns	PS00171	Triosephosphate isomerase active site.
171	181	InterPro	IPR020861	Triosephosphate isomerase, active site
7	255	FunFam	G3DSA:3.20.20.70:FF:000016	Triosephosphate isomerase
13	243	NCBIfam	TIGR00419	triose-phosphate isomerase
13	243	InterPro	IPR000652	Triosephosphate isomerase

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 #6

0.711

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Surrounding area

Site 2 FPocket #4

0.557

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Surrounding area

Site 3 FPocket #1

0.354

Likely same site as P2Rank 2 1.8 Å 17 shared residues 94% of smaller site

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Surrounding area

Site 4 FPocket #3

0.334

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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

0.612

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Surrounding area

Site 2 P2Rank #2

0.239

Likely same site as FPocket 1 1.8 Å 17 shared residues 94% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.012

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Surrounding area

All structural evidence 0 experimental · 1 predicted

Structural evidence

0 + 1

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 HT085_RS00085	AlphaFold DB	—	—	full sequence	—	Viewing

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.

60 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 10 records from similar proteins

Structural ligands 10 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

13P PDB via homolog 170.1 Da · LogP -1.34 · TPSA 104.1 Open detail RCSB PDB

2PG PDB via homolog Detail RCSB PDB

3PG PDB via homolog Detail RCSB PDB

3PY PDB via homolog Detail RCSB PDB

DTT 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
13P RCSB PDB	5UJW	Q5NII7	170.1 Da LogP -1.34 TPSA 104.1	✓ Ro5	✓ Clean	`C(C(=O)COP(=O)(O)O)O`
2PG RCSB PDB	3UWV	Q6GIL6	186.1 Da LogP -1.46 TPSA 124.3	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)OP(=O)(O)O)O`
3PG RCSB PDB	3UWW	Q6GIL6	186.1 Da LogP -1.46 TPSA 124.3	✓ Ro5	✓ Clean	`C([C@H](C(=O)O)O)OP(=O)(O)O`
3PY RCSB PDB	1O5X	Q07412	104.1 Da LogP -1.37 TPSA 74.6	✓ Ro5	✓ Clean	`C(C(=O)C(=O)O)O`
DTT RCSB PDB	3UWW	Q6GIL6	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`
G2H RCSB PDB	3UWZ	Q6GIL6	172.1 Da LogP -1.55 TPSA 107.2	✓ Ro5	✓ Clean	`C(C(CO)OP(=O)(O)O)O`
G3H RCSB PDB	1M7P	Q07412	170.1 Da LogP -1.34 TPSA 104.1	✓ Ro5	✓ Clean	`C([C@H](C=O)O)OP(=O)(O)O`
G3P RCSB PDB	3UWU	Q6GIL6	172.1 Da LogP -1.55 TPSA 107.2	✓ Ro5	✓ Clean	`C([C@H](COP(=O)(O)O)O)O`
PGA RCSB PDB	1BTM	P00943	156.0 Da LogP -0.82 TPSA 104.1	✓ Ro5	✓ Clean	`C(C(=O)O)OP(=O)(O)O`
PO3 RCSB PDB	1O5X	Q07412	79.0 Da LogP -1.64 TPSA 63.2	✓ Ro5	✓ Clean	`[O-][P-](=O)[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
ZINC1532902 ZINC	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106 ZINC	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC3593496 ZINC	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497 ZINC	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC5975509 ZINC	0.640	202.1 Da LogP -2.19 TPSA 127.5	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)CO`
ZINC3869233 ZINC	0.630	266.0 Da LogP -1.34 TPSA 170.8	✓ Ro5	✓ Clean	`O=C(O)[C@H](COP(=O)(O)O)OP(=O)(O)O`
ZINC3869234 ZINC	0.630	266.0 Da LogP -1.34 TPSA 170.8	✓ Ro5	✓ Clean	`O=C(O)[C@@H](COP(=O)(O)O)OP(=O)(O)O`
ZINC14686440 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444 ZINC	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC2516111 ZINC	0.593	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`
ZINC2522704 ZINC	0.593	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	0.593	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`
ZINC12501558 ZINC	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(…`
ZINC12501560 ZINC	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O…`
ZINC12501562 ZINC	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)…`
ZINC1532623 ZINC	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(…`
ZINC2545091 ZINC	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O…`
ZINC3869604 ZINC	0.586	276.1 Da LogP -3.38 TPSA 185.0	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC13398039 ZINC	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012 ZINC	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC4095590 ZINC	0.567	215.1 Da LogP -1.57 TPSA 122.2	✓ Ro5	✓ Clean	`NCCO[P@@](=O)(O)OC[C@H](O)CO`
ZINC4095591 ZINC	0.567	215.1 Da LogP -1.57 TPSA 122.2	✓ Ro5	✓ Clean	`NCCO[P@@](=O)(O)OC[C@@H](O)CO`
ZINC146315135 ZINC	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336 ZINC	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC1850353 ZINC	0.556	206.1 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC(O)(CC(=O)O)CC(=O)O`
ZINC1676569 ZINC	0.542	224.2 Da LogP 2.56 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)CC(CC(C)C)OP(=O)(O)O`
ZINC1680142 ZINC	0.533	212.1 Da LogP -0.34 TPSA 96.2	✓ Ro5	✓ Clean	`C=CCOC[C@@H](O)COP(=O)(O)O`
ZINC4887586 ZINC	0.533	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	0.533	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	0.533	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	0.533	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`
ZINC5426687 ZINC	0.533	212.1 Da LogP -0.34 TPSA 96.2	✓ Ro5	✓ Clean	`C=CCOC[C@H](O)COP(=O)(O)O`
ZINC100067589 ZINC	0.531	334.2 Da LogP -4.34 TPSA 197.4	1 viol.	✓ Clean	`O=[P@@](O)(OC[C@H](O)CO)O[C@H]1[C@H](O)[C@@H](O…`
ZINC100620818 ZINC	0.531	334.2 Da LogP -4.34 TPSA 197.4	1 viol.	✓ Clean	`O=[P@@](O)(OC[C@H](O)CO)O[C@H]1[C@@H](O)[C@@H](…`
ZINC13398014 ZINC	0.522	220.2 Da LogP -1.07 TPSA 110.1	✓ Ro5	✓ Clean	`COC(=O)CC(O)(CC(=O)OC)C(=O)O`
ZINC3861629 ZINC	0.522	206.1 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C(O)(CC(=O)O)CC(=O)O`
ZINC5575424 ZINC	0.520	200.0 Da LogP -1.37 TPSA 141.4	✓ Ro5	✓ Clean	`O=C(O)C(OP(=O)(O)O)C(=O)O`
ZINC100065511 ZINC	0.516	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	0.516	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	0.516	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`
ZINC12502210 ZINC	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC12502212 ZINC	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC12502214 ZINC	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC12502216 ZINC	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC4523251 ZINC	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@@H](O)COP(…`
ZINC4523255 ZINC	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@H](O)COP(=…`
ZINC4523257 ZINC	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@@H](O)COP(=…`
ZINC4523259 ZINC	0.516	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)COP(=O…`
ZINC85994845 ZINC	0.516	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`

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.

HT085_RS00085

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

Binding-site evidence

Sequence

Functional annotations

Enzyme Commission (EC)

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · FPocket

Binding pockets · P2Rank

Structural evidence

Ligand evidence