Protein target profile

HT085_RS00385

HAD-IA family hydrolase

Genome: NZ_AP023069.1 Gene: E8M63_05115 TUM19854C_00640 3D evidence: AlphaFold DB model UniProt A0AAX2C0Z5

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Length 219

Direct ligand evidence 0 27 total records

Functional annotation 0 EC 3 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.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Structure available AlphaFold DB model Ligand evidence via structure/bioactivity 10 structural and 0 bioactivity records.

Risks to review

No major risk signal surfaced in the loaded evidence.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. No FPocket pocket score No selected computational pocket-druggability value is available.

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: No hit
Gut microbiome off-target: Hit

Essentiality

Essential (DEG): N

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 Medium

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MTPPKLIIFDWDGTLADTTQPIIDTMRRSFAECGFPPPEAERVRSLIGYSLPEIIRALLEMPSEAAVADIARTYSAHYLNPNNRNMTLFPDALPCLDKLKAQGFRLAVATGKGRAGLDNAISQTATGGYWLATACAGEYPSKPSPEMVFGLCGELGLDPKEALVVGDTAHDLHMAANAGAAAVGVATGAHSREQLLGAPHLAVLDGLSELPGFLARHYA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0008967 Catalysis of the reaction: 2-phosphoglycolate + H2O = glycolate + phosphate.
GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
1	212	PANTHER	PTHR43434	PHOSPHOGLYCOLATE PHOSPHATASE
7	185	Pfam	PF13419	Haloacid dehalogenase-like hydrolase
7	185	InterPro	IPR041492	Haloacid dehalogenase-like hydrolase
133	179	NCBIfam	TIGR01549	HAD-IA family hydrolase
133	179	InterPro	IPR006439	HAD hydrolase, subfamily IA
4	215	SFLD	SFLDG01135	C1.5.6: HAD, Beta-PGM, Phosphatase Like
4	215	SFLD	SFLDG01129	C1.5: HAD, Beta-PGM, Phosphatase Like
5	214	SUPERFAMILY	SSF56784	HAD-like
5	214	InterPro	IPR036412	HAD-like superfamily
19	83	Gene3D	G3DSA:1.10.150.240	Putative phosphatase; domain 2
19	83	InterPro	IPR023198	Phosphoglycolate phosphatase-like, domain 2
7	199	Gene3D	G3DSA:3.40.50.1000	-
7	199	InterPro	IPR023214	HAD 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

0.667

Likely same site as P2Rank 1 1.9 Å 19 shared residues 86% of smaller site

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Surrounding area

Site 2 FPocket #4

0.386

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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

0.605

Likely same site as FPocket 1 1.9 Å 19 shared residues 86% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.099

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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_RS00385	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.

27 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 17 similarity-based ZINC candidates

Best available ligand signal

ALF PDB via homolog 103.0 Da · LogP 1.30 · TPSA 0.0 Open detail RCSB PDB

BEF PDB via homolog Detail RCSB PDB

BO3 PDB via homolog Detail RCSB PDB

ESA PDB via homolog Detail RCSB PDB

MGF 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
ALF RCSB PDB	6H8W	P71447	103.0 Da LogP 1.30 TPSA 0.0	✓ Ro5	✓ Clean	`F[Al-](F)(F)F`
BEF RCSB PDB	2WFA	P71447	66.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`[Be-](F)(F)F`
BO3 RCSB PDB	4EX7	B6SEG4	61.8 Da LogP -2.05 TPSA 60.7	✓ Ro5	✓ Clean	`B(O)(O)O`
ESA RCSB PDB	1RDF	O31156	110.1 Da LogP -0.11 TPSA 54.4	✓ Ro5	✓ Clean	`CCS(=O)(=O)O`
MGF RCSB PDB	6H8X	P71447	81.3 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`F[Mg-](F)F`
POA RCSB PDB	1SWW	O31156	124.0 Da LogP -0.64 TPSA 74.6	✓ Ro5	✓ Clean	`C(C=O)P(=O)(O)O`
UVW RCSB PDB	6H91	P71447	140.0 Da LogP -0.36 TPSA 83.8	✓ Ro5	✓ Clean	`CC(=O)OP(=O)(O)O`
VO4 RCSB PDB	4KNW	Q8TBE9	114.9 Da LogP -3.69 TPSA 86.2	✓ Ro5	✓ Clean	`[O-][V](=O)([O-])[O-]`
VSO RCSB PDB	1RQL	O31156	108.1 Da LogP 0.02 TPSA 54.4	✓ Ro5	✓ Clean	`C=CS(=O)(=O)O`
WO4 RCSB PDB	1FEZ	O31156	247.8 Da LogP -2.62 TPSA 80.3	✓ Ro5	✓ Clean	`[O-][W](=O)(=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`
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(=…`
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`
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`
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`
ZINC100969993 ZINC	0.500	359.5 Da LogP 2.70 TPSA 123.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC100969996 ZINC	0.500	359.5 Da LogP 2.70 TPSA 123.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC1711854 ZINC	0.500	248.2 Da LogP -0.13 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)CC(CC(=O)O)(CC(=O)O)CC(=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.