Protein profile

KP13_00592

L-rhamnose isomerase

Genome: KpKP13

Gene: AHE47067.1 rhaA Structure source: AlphaFold + ColabFold UniProt A0A0H3GLE3

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Amino acids 419

Annotations 7

Features 11

PDB binders 2

Druggability 0.455

Overview

Basic information about this protein and its source genome.

Accession: KP13_00592
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE47067.1 rhaA
Status: annotated
Amino acids: 419
Structure source: AlphaFold + ColabFold

5.3.1.14

GO:0019299 OBSOLETE. The chemical reactions and pathways involving rhamnose, the hexose 6-deoxy-L-mannose. Rhamnose occurs commonly as a compound of plant glycosides, in polysaccharides of gums and mucilages, and in bacterial polysaccharides. It is also a component of some plant cell wall polysaccharides and frequently acts as the sugar components of flavonoids. GO:0030145 Binding to a manganese ion (Mn). GO:0008740 Catalysis of the reaction: L-rhamnose = L-rhamnulose. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0019324 The chemical reactions and pathways involving L-lyxose, the L-enantiomer of aldopentose lyxo-pentose, the C-2 epimer of xylose. GO:0019301 The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.94

Selected Druggability evidence

AlphaFold / UniProt model

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 0.455

Structure A0A0H3GLE3

Pocket Pocket 2

P2Rank 0.601

Structure A0A0H3GLE3

Pocket Pocket 1

ColabFold model

FPocket 0.498 · Pocket 1

P2Rank 0.733 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 816 / 4744 genomes with a hit

Normalized 0.172

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

5.3.1.14

Gene Ontology (GO)

GO:0019299 OBSOLETE. The chemical reactions and pathways involving rhamnose, the hexose 6-deoxy-L-mannose. Rhamnose occurs commonly as a compound of plant glycosides, in polysaccharides of gums and mucilages, and in bacterial polysaccharides. It is also a component of some plant cell wall polysaccharides and frequently acts as the sugar components of flavonoids.
GO:0030145 Binding to a manganese ion (Mn).
GO:0008740 Catalysis of the reaction: L-rhamnose = L-rhamnulose.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0019324 The chemical reactions and pathways involving L-lyxose, the L-enantiomer of aldopentose lyxo-pentose, the C-2 epimer of xylose.
GO:0019301 The chemical reactions and pathways resulting in the breakdown of rhamnose, the hexose 6-deoxy-L-mannose.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records

Show feature table

Start	End	DB	Term	Name
1	419	FunFam	G3DSA:3.20.20.150:FF:000006	L-rhamnose isomerase
4	418	SUPERFAMILY	SSF51658	Xylose isomerase-like
4	418	InterPro	IPR036237	Xylose isomerase-like superfamily
3	418	Pfam	PF06134	L-rhamnose isomerase (RhaA)
3	418	InterPro	IPR009308	Rhamnose isomerase
5	418	NCBIfam	TIGR01748	L-rhamnose isomerase
5	418	InterPro	IPR009308	Rhamnose isomerase
1	419	Hamap	MF_00541	L-rhamnose isomerase [rhaA].
1	419	InterPro	IPR009308	Rhamnose isomerase
1	419	Gene3D	G3DSA:3.20.20.150	-
2	418	PANTHER	PTHR30268	L-RHAMNOSE ISOMERASE

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

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GLE3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00592	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
2				0.455

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	10.88	0.584
2	3.04	0.1
3	2.6	0.075

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
1				0.498

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	12.61	0.656
2	3.47	0.126
3	1.99	0.042
4	1.72	0.03

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.

39 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.

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
RNS	1DE6	P32170	164.2 Da LogP -2.35 TPSA 98.0	✓ Ro5	✓ Clean	`C[C@@H]([C@@H]([C@H]([C@H](C=O)O)O)O)O`
RNT	1DE5	P32170	166.2 Da LogP -2.56 TPSA 101.2	✓ Ro5	✓ Clean	`C[C@@H]([C@@H]([C@H]([C@H](CO)O)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
ZINC100055463	0.647	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC100064885	0.647	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC17780060	0.647	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC17952732	0.647	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC18042331	0.647	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H]…`
ZINC18120313	0.647	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC3979006	0.647	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC4403103	0.647	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC4403105	0.647	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC4403107	0.647	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@…`
ZINC9212412	0.647	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@@H](O)CO`
ZINC216185927	0.522	209.2 Da LogP -3.02 TPSA 104.4	✓ Ro5	✓ Clean	`CN(C)C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC216185976	0.522	209.2 Da LogP -3.02 TPSA 104.4	✓ Ro5	✓ Clean	`CN(C)C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC216186168	0.522	224.3 Da LogP -2.87 TPSA 101.2	✓ Ro5	✓ Clean	`C[N+](C)(C)C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC216186206	0.522	224.3 Da LogP -2.87 TPSA 101.2	✓ Ro5	✓ Clean	`C[N+](C)(C)C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC25624721	0.522	209.2 Da LogP -3.02 TPSA 104.4	✓ Ro5	✓ Clean	`CN(C)C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC25624980	0.522	224.3 Da LogP -2.87 TPSA 101.2	✓ Ro5	✓ Clean	`C[N+](C)(C)C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC4566610	0.522	209.2 Da LogP -3.02 TPSA 104.4	✓ Ro5	✓ Clean	`CN(C)C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC4566614	0.522	224.3 Da LogP -2.87 TPSA 101.2	✓ Ro5	✓ Clean	`C[N+](C)(C)C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC5066653	0.520	312.5 Da LogP 1.17 TPSA 80.9	✓ Ro5	✓ Clean	`CC(C)CSC(SCC(C)C)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC5066655	0.520	312.5 Da LogP 1.17 TPSA 80.9	✓ Ro5	✓ Clean	`CC(C)CSC(SCC(C)C)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC5066658	0.520	312.5 Da LogP 1.17 TPSA 80.9	✓ Ro5	✓ Clean	`CC(C)CSC(SCC(C)C)[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC5066661	0.520	312.5 Da LogP 1.17 TPSA 80.9	✓ Ro5	✓ Clean	`CC(C)CSC(SCC(C)C)[C@@H](O)[C@@H](O)[C@H](O)CO`
ZINC14944599	0.500	256.4 Da LogP -0.11 TPSA 80.9	✓ Ro5	✓ Clean	`CCSC(SCC)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC1868590	0.500	256.4 Da LogP -0.11 TPSA 80.9	✓ Ro5	✓ Clean	`CCSC(SCC)[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC3137815	0.500	256.4 Da LogP -0.11 TPSA 80.9	✓ Ro5	✓ Clean	`CCSC(SCC)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC3843093	0.500	256.4 Da LogP -0.11 TPSA 80.9	✓ Ro5	✓ Clean	`CCSC(SCC)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC4691943	0.500	256.4 Da LogP -0.11 TPSA 80.9	✓ Ro5	✓ Clean	`CCSC(SCC)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC4691944	0.500	256.4 Da LogP -0.11 TPSA 80.9	✓ Ro5	✓ Clean	`CCSC(SCC)[C@@H](O)[C@@H](O)[C@H](O)CO`
ZINC5201837	0.500	345.3 Da LogP -6.55 TPSA 214.3	2 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@H](…`
ZINC5201838	0.500	345.3 Da LogP -6.55 TPSA 214.3	2 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@@H]…`
ZINC5201839	0.500	345.3 Da LogP -6.55 TPSA 214.3	2 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@H](…`
ZINC5201841	0.500	345.3 Da LogP -6.55 TPSA 214.3	2 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@@H]…`
ZINC5732420	0.500	212.2 Da LogP -3.61 TPSA 130.6	1 viol.	✓ Clean	`CO[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC5732422	0.500	212.2 Da LogP -3.61 TPSA 130.6	1 viol.	✓ Clean	`CO[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC5732426	0.500	212.2 Da LogP -3.61 TPSA 130.6	1 viol.	✓ Clean	`CO[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC5732428	0.500	212.2 Da LogP -3.61 TPSA 130.6	1 viol.	✓ Clean	`CO[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`

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.