Protein profile

KP13_05482

Hydantoin racemase

Genome: KpKP13

Gene: hyuE AHE44487.1 Structure source: Experimental + ColabFold UniProt A6T9E8

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Amino acids 240

Annotations 2

Features 5

PDB binders 2

Druggability 0.515

Overview

Basic information about this protein and its source genome.

Accession: KP13_05482
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: hyuE AHE44487.1
Status: annotated
Amino acids: 240
Structure source: Experimental + ColabFold

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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 53.556
DEG E-value: 2.95e-84
Localization: Unknown
ColabFold pLDDT: 98.1

Selected Druggability evidence

PDB experimental structure

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its 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

Normalized 0.011

Sequence

Primary amino-acid sequence viewer.

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

2 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 3QVK	X-ray	20.00 Å	-	—	PDBe RCSB PDBj File	Viewing
PDB 3QVL	X-ray	20.00 Å	-	—	PDBe RCSB PDBj File	Loaded
ColabFold KP13_05482	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
5				0.67
10				0.583
12				0.515
25				0.222

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
7				0.49
9				0.245

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	6.4	0.322
2	1.71	0.03
3	0.88	0.004

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

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

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
2AL	3QVK Open crystal	156.1 Da LogP -1.70 TPSA 113.6	✓ Ro5	✓ Clean	`C1(=O)C(=NC(=O)N1)NC(=O)N`
5HY	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	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	0.576	206.2 Da LogP 0.89 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)C[C@@H]1Nc2ccccc2NC1=O`
ZINC264007	0.576	206.2 Da LogP 0.89 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)C[C@H]1Nc2ccccc2NC1=O`
ZINC5328959	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	0.559	206.2 Da LogP 1.34 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)C[C@@H]1NC(=O)Nc2ccccc21`
ZINC238655369	0.559	206.2 Da LogP 1.34 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)C[C@H]1NC(=O)Nc2ccccc21`
ZINC9256923	0.559	211.2 Da LogP -0.79 TPSA 78.5	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](CC(=O)N2CCCC2)N1`
ZINC9256924	0.559	211.2 Da LogP -0.79 TPSA 78.5	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](CC(=O)N2CCCC2)N1`
ZINC613556	0.556	233.2 Da LogP 0.22 TPSA 87.3	✓ Ro5	✓ Clean	`O=C(C[C@@H]1NC(=O)NC1=O)Nc1ccccc1`
ZINC613557	0.556	233.2 Da LogP 0.22 TPSA 87.3	✓ Ro5	✓ Clean	`O=C(C[C@H]1NC(=O)NC1=O)Nc1ccccc1`
ZINC1298531	0.543	225.2 Da LogP -0.40 TPSA 78.5	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](CC(=O)N2CCCCC2)N1`
ZINC1298533	0.543	225.2 Da LogP -0.40 TPSA 78.5	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](CC(=O)N2CCCCC2)N1`
ZINC1298528	0.528	227.2 Da LogP -1.56 TPSA 87.7	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](CC(=O)N2CCOCC2)N1`
ZINC1298530	0.528	227.2 Da LogP -1.56 TPSA 87.7	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](CC(=O)N2CCOCC2)N1`
ZINC1875304691	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	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	0.514	234.2 Da LogP 0.21 TPSA 95.5	✓ Ro5	✓ Clean	`O=C(O)C[C@@H]1NC(=O)c2ccccc2NC1=O`
ZINC12900439	0.514	234.2 Da LogP 0.21 TPSA 95.5	✓ Ro5	✓ Clean	`O=C(O)C[C@H]1NC(=O)c2ccccc2NC1=O`
ZINC65504945	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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.