Protein target profile

KP13_05482

Hydantoin racemase

Genome: KpKP13 Gene: AHE44487.1 hyuE 3D evidence: Experimental + ColabFold model UniProt A6T9E8

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Length 240

Pocket druggability 0.515

Direct ligand evidence 2 38 total records

Functional annotation 0 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

Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Direct ligand evidence 2 direct ligand records. Strong known ligand: co-crystal structure 2 PDB record(s) show a ligand actually co-crystallized with this exact protein - real experimental evidence, not a computational prediction. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Review the complete evidence below

Risks to review

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: No hit
Gut microbiome similarity: 1.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 53.556 Higher values support similarity to known essential genes.
DEG E-value: 2.95e-84 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Unknown

Structure confidence

ColabFold pLDDT: 98.1 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.515

Structure 3QVK

Pocket Pocket 4

P2Rank 0.4

Structure 3QVL

Pocket Pocket 1

ColabFold model

FPocket 0.49 · Pocket 7

P2Rank 0.422 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 51 / 4744 genomes with a hit

Prevalence 1.1%

Cross-references

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

Sequence

UniProt A6T9E8

Structure

PDB 3QVJ PDB 3QVK PDB 3QVL

Sequence

Primary amino-acid sequence viewer.

MINPNTSLAMTETIGAAARAVAAPGTEILAVSPRAGVPSIEGHFDEAIAAVGVLEQIKAGREQGVDGHVIACFGDPGLLAARELAQGPVIGIAEAAMHMATMVATRFSIVTTLPRTLIIARHLLHQYGFHQHCAALHAIDLPVLALEDGSGLAQEKVRERCIRALKEDGSGAIVLGCGGMATLAQELTRELRVPVIDGVSAAVKMVESLVALGLATSKHGDLAFPEKKALSGQFQSLNPF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0036361 OBSOLETE. Catalysis of the interconversion of the two enantiomers of a chiral amino acid or amino acid derivative.
GO:0006807 OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

5 records

Show feature table

Start	End	DB	Term	Name
1	226	PANTHER	PTHR28047	PROTEIN DCG1
1	234	FunFam	G3DSA:3.40.50.12500:FF:000001	Putative hydantoin racemase
1	240	Gene3D	G3DSA:3.40.50.12500	-
1	205	Pfam	PF01177	Asp/Glu/Hydantoin racemase
1	205	InterPro	IPR015942	Asp/Glu/hydantoin racemase

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 #4

0.515

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Surrounding area

Site 2 FPocket #11

0.222

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Surrounding area

Binding pockets · FPocket

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

Site 1 FPocket #7

0.49

Likely same site as P2Rank 2 1.9 Å 18 shared residues 100% of smaller site

Unusual size

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Surrounding area

Site 2 FPocket #9

0.245

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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

0.422

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Surrounding area

Site 2 P2Rank #2

0.252

Likely same site as FPocket 7 1.9 Å 18 shared residues 100% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.035

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Surrounding area

All structural evidence 3 experimental · 1 predicted

Structural evidence

3 + 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
PDB 3QVJ	X-ray	—	A	—	PDBe RCSB PDBj File	Loaded
PDB 3QVK	X-ray	—	A	—	PDBe RCSB PDBj File	Viewing
PDB 3QVL	X-ray	—	A	—	PDBe RCSB PDBj File	Loaded
ColabFold KP13_05482	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.

38 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 2 same-protein records

Transferred evidence 0 records from similar proteins

Structural ligands 2 2 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 36 similarity-based ZINC candidates

Best available ligand signal

2AL PDB co-crystal 156.1 Da · LogP -1.70 · TPSA 113.6 Open detail RCSB PDB

5HY PDB co-crystal Detail RCSB PDB

ZINC1738553 ZINC proposed compound · Tanimoto 0.576 Detail ZINC

ZINC264004 ZINC proposed compound · Tanimoto 0.576 Detail ZINC

ZINC264007 ZINC proposed compound · Tanimoto 0.576 Detail ZINC

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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
2AL RCSB PDB	3QVK Open crystal	156.1 Da LogP -1.70 TPSA 113.6	✓ Ro5	✓ Clean	`C1(=O)C(=NC(=O)N1)NC(=O)N`
5HY RCSB PDB	3QVL Open crystal	158.1 Da LogP -1.33 TPSA 95.5	✓ Ro5	✓ Clean	`C([C@@H]1C(=O)NC(=O)N1)C(=O)O`

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.

No PDB ligands found through similar proteins.

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
ZINC1738553 ZINC	0.576	200.2 Da LogP -2.22 TPSA 130.4	✓ Ro5	✓ Clean	`NC(=O)NC(=O)C[C@@H]1NC(=O)NC1=O`
ZINC264004 ZINC	0.576	206.2 Da LogP 0.89 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)C[C@@H]1Nc2ccccc2NC1=O`
ZINC264007 ZINC	0.576	206.2 Da LogP 0.89 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)C[C@H]1Nc2ccccc2NC1=O`
ZINC5328959 ZINC	0.576	200.2 Da LogP -2.22 TPSA 130.4	✓ Ro5	✓ Clean	`NC(=O)NC(=O)C[C@H]1NC(=O)NC1=O`
ZINC238634505 ZINC	0.559	206.2 Da LogP 1.34 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)C[C@@H]1NC(=O)Nc2ccccc21`
ZINC238655369 ZINC	0.559	206.2 Da LogP 1.34 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)C[C@H]1NC(=O)Nc2ccccc21`
ZINC9256923 ZINC	0.559	211.2 Da LogP -0.79 TPSA 78.5	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](CC(=O)N2CCCC2)N1`
ZINC9256924 ZINC	0.559	211.2 Da LogP -0.79 TPSA 78.5	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](CC(=O)N2CCCC2)N1`
ZINC613556 ZINC	0.556	233.2 Da LogP 0.22 TPSA 87.3	✓ Ro5	✓ Clean	`O=C(C[C@@H]1NC(=O)NC1=O)Nc1ccccc1`
ZINC613557 ZINC	0.556	233.2 Da LogP 0.22 TPSA 87.3	✓ Ro5	✓ Clean	`O=C(C[C@H]1NC(=O)NC1=O)Nc1ccccc1`
ZINC1298531 ZINC	0.543	225.2 Da LogP -0.40 TPSA 78.5	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](CC(=O)N2CCCCC2)N1`
ZINC1298533 ZINC	0.543	225.2 Da LogP -0.40 TPSA 78.5	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](CC(=O)N2CCCCC2)N1`
ZINC1298528 ZINC	0.528	227.2 Da LogP -1.56 TPSA 87.7	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](CC(=O)N2CCOCC2)N1`
ZINC1298530 ZINC	0.528	227.2 Da LogP -1.56 TPSA 87.7	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](CC(=O)N2CCOCC2)N1`
ZINC1875304691 ZINC	0.528	276.2 Da LogP -0.12 TPSA 95.5	✓ Ro5	✓ Clean	`O=C(O)C[C@@H]1NC(=O)[C@H](CC2CC(F)(F)C2)NC1=O`
ZINC1875304692 ZINC	0.528	276.2 Da LogP -0.12 TPSA 95.5	✓ Ro5	✓ Clean	`O=C(O)C[C@@H]1NC(=O)[C@@H](CC2CC(F)(F)C2)NC1=O`
ZINC11764459 ZINC	0.514	234.2 Da LogP 0.21 TPSA 95.5	✓ Ro5	✓ Clean	`O=C(O)C[C@@H]1NC(=O)c2ccccc2NC1=O`
ZINC12900439 ZINC	0.514	234.2 Da LogP 0.21 TPSA 95.5	✓ Ro5	✓ Clean	`O=C(O)C[C@H]1NC(=O)c2ccccc2NC1=O`
ZINC65504945 ZINC	0.514	269.3 Da LogP 1.01 TPSA 78.5	✓ Ro5	✓ Clean	`CCCCN(CCCC)C(=O)C[C@H]1NC(=O)NC1=O`
ZINC65504949 ZINC	0.514	269.3 Da LogP 1.01 TPSA 78.5	✓ Ro5	✓ Clean	`CCCCN(CCCC)C(=O)C[C@@H]1NC(=O)NC1=O`
ZINC4717907 ZINC	0.513	277.2 Da LogP -0.08 TPSA 124.6	✓ Ro5	✓ Clean	`O=C(C[C@H]1NC(=O)NC1=O)Nc1ccc(C(=O)O)cc1`
ZINC4717908 ZINC	0.513	277.2 Da LogP -0.08 TPSA 124.6	✓ Ro5	✓ Clean	`O=C(C[C@@H]1NC(=O)NC1=O)Nc1ccc(C(=O)O)cc1`
ZINC1123643 ZINC	0.500	267.7 Da LogP 0.88 TPSA 87.3	✓ Ro5	✓ Clean	`O=C(C[C@@H]1NC(=O)NC1=O)Nc1ccc(Cl)cc1`
ZINC1123644 ZINC	0.500	267.7 Da LogP 0.88 TPSA 87.3	✓ Ro5	✓ Clean	`O=C(C[C@H]1NC(=O)NC1=O)Nc1ccc(Cl)cc1`
ZINC183055574 ZINC	0.500	225.2 Da LogP -0.38 TPSA 78.5	✓ Ro5	✓ Clean	`C=C(C)CN(C)C(=O)C[C@@H]1NC(=O)NC1=O`
ZINC2860503 ZINC	0.500	251.2 Da LogP 0.36 TPSA 87.3	✓ Ro5	✓ Clean	`O=C(C[C@@H]1NC(=O)NC1=O)Nc1ccc(F)cc1`
ZINC2860504 ZINC	0.500	251.2 Da LogP 0.36 TPSA 87.3	✓ Ro5	✓ Clean	`O=C(C[C@H]1NC(=O)NC1=O)Nc1ccc(F)cc1`
ZINC395626 ZINC	0.500	262.3 Da LogP -0.31 TPSA 95.5	✓ Ro5	✓ Clean	`O=C(O)C[C@@H]1NC(=O)[C@H](Cc2ccccc2)NC1=O`
ZINC395627 ZINC	0.500	262.3 Da LogP -0.31 TPSA 95.5	✓ Ro5	✓ Clean	`O=C(O)C[C@@H]1NC(=O)[C@@H](Cc2ccccc2)NC1=O`
ZINC395628 ZINC	0.500	262.3 Da LogP -0.31 TPSA 95.5	✓ Ro5	✓ Clean	`O=C(O)C[C@H]1NC(=O)[C@H](Cc2ccccc2)NC1=O`
ZINC395629 ZINC	0.500	262.3 Da LogP -0.31 TPSA 95.5	✓ Ro5	✓ Clean	`O=C(O)C[C@H]1NC(=O)[C@@H](Cc2ccccc2)NC1=O`
ZINC48688137 ZINC	0.500	267.3 Da LogP 0.77 TPSA 78.5	✓ Ro5	✓ Clean	`CN(C(=O)C[C@@H]1NC(=O)NC1=O)C1CCCCCC1`
ZINC6036037 ZINC	0.500	214.2 Da LogP -0.90 TPSA 95.5	✓ Ro5	✓ Clean	`CC(C)[C@@H]1NC(=O)[C@H](CC(=O)O)NC1=O`
ZINC819967380 ZINC	0.500	271.3 Da LogP -0.80 TPSA 124.6	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)C[C@@H]1NC(=O)NC1=O)C(=O)O`
ZINC819967381 ZINC	0.500	271.3 Da LogP -0.80 TPSA 124.6	✓ Ro5	✓ Clean	`CC(C)C[C@@H](NC(=O)C[C@@H]1NC(=O)NC1=O)C(=O)O`
ZINC95461505 ZINC	0.500	212.2 Da LogP -0.30 TPSA 84.5	✓ Ro5	✓ Clean	`C/C=C/COC(=O)C[C@@H]1NC(=O)NC1=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.