Protein profile

VK055_0444

xylose isomerase-like TIM barrel family protein

Genome: KpATCC43816

Gene: AIK79070.1 Structure source: AlphaFold + ColabFold UniProt A0A0C7KKB1

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Amino acids 317

Annotations 3

Features 6

PDB binders 14

Druggability 0.582

Overview

Basic information about this protein and its source genome.

Accession: VK055_0444
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79070.1
Status: annotated
Amino acids: 317
Structure source: AlphaFold + ColabFold

5.3.1.5

GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks. GO:0009045 Catalysis of the reaction: alpha-D-xylose = alpha-D-xylulofuranose.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: No hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.18

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 0.582

Structure A0A0C7KKB1

Pocket Pocket 2

P2Rank 0.6

Structure A0A0C7KKB1

Pocket Pocket 1

ColabFold model

FPocket 0.627 · Pocket 2

P2Rank 0.607 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 0 / 4744 genomes with a hit

Normalized 0

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 2 GO

Enzyme Commission (EC)

5.3.1.5

Gene Ontology (GO)

GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks.
GO:0009045 Catalysis of the reaction: alpha-D-xylose = alpha-D-xylulofuranose.

Sequence Features

Domain/signature hits from InterPro and related databases.

6 records

Show feature table

Start	End	DB	Term	Name
6	316	Gene3D	G3DSA:3.20.20.150	-
37	279	Pfam	PF01261	Xylose isomerase-like TIM barrel
37	279	InterPro	IPR013022	Xylose isomerase-like, TIM barrel domain
1	315	SUPERFAMILY	SSF51658	Xylose isomerase-like
1	315	InterPro	IPR036237	Xylose isomerase-like superfamily
76	243	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_A0A0C7KKB1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0444	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				0.582
3				0.185
16				0.003
1				0.0

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	13.35	0.6
2	6.43	0.272
3	4.55	0.161
4	2.26	0.046
5	1.43	0.015

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
9				0.005
4				0.0
6				0.0
7				0.0

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	13.55	0.607
2	4.96	0.184
3	4.88	0.18
4	2.5	0.057
5	2.02	0.037

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.

64 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
03W	3U3H	P24300	108.1 Da LogP -2.35 TPSA 80.9	✓ Ro5	✓ Clean	`C([C@H](C(O)O)O)O`
3MF	1XYC	P15587	194.2 Da LogP -2.72 TPSA 107.2	✓ Ro5	✓ Clean	`CO[C@@H]([C@@H]([C@@H](CO)O)O)C(=O)CO`
AOS	2I57	Q75WH8	180.2 Da LogP -3.38 TPSA 118.2	✓ Ro5	✓ Clean	`C([C@H]([C@H]([C@H]([C@H](C=O)O)O)O)O)O`
DIG	1DID	P12070	163.2 Da LogP -2.97 TPSA 93.0	✓ Ro5	✓ Clean	`C([C@H]1[C@H]([C@@H]([C@H](N1)CO)O)O)O`
HYA	2GYI	P15587	151.1 Da LogP -1.95 TPSA 113.5	✓ Ro5	✓ Clean	`C([C@H]([C@@H](/C(=N/O)/O)O)O)O`
KR	1O1H	P24300	83.8 Da LogP 0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Kr]`
LAI	4QDW	P24300	150.1 Da LogP -2.74 TPSA 98.0	✓ Ro5	✓ Clean	`C([C@@H]([C@@H]([C@H](C=O)O)O)O)O`
MQD	1OAD	P24300	134.2 Da LogP -0.50 TPSA 60.7	✓ Ro5	✓ Clean	`C[C@@H](C[C@@](C)(CO)O)O`
NOJ	1DIE	P12070	163.2 Da LogP -2.97 TPSA 93.0	✓ Ro5	✓ Clean	`C1[C@@H]([C@H]([C@@H]([C@H](N1)CO)O)O)O`
PSJ	3ITV	Q75WH8	180.2 Da LogP -3.38 TPSA 118.2	✓ Ro5	✓ Clean	`C([C@H]([C@H]([C@H](C(=O)CO)O)O)O)O`
RNS	2I56	Q75WH8	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`
THE	1XIJ	P24300	135.1 Da LogP -3.55 TPSA 100.8	✓ Ro5	✓ Clean	`C([C@H]([C@@H](C(=O)[O-])O)O)O`
XLS	6XIM	P12851	150.1 Da LogP -2.74 TPSA 98.0	✓ Ro5	✓ Clean	`C([C@H]([C@@H]([C@H](C=O)O)O)O)O`
XUL	1XII	P24300	150.1 Da LogP -2.74 TPSA 98.0	✓ Ro5	✓ Clean	`C([C@H]([C@@H](C(=O)CO)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
ZINC100056793	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC100056796	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC12953159	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC12953162	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC12953168	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC13522675	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC13522684	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)CO`
ZINC4353166	0.950	240.2 Da LogP -4.66 TPSA 158.7	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O…`
ZINC4353167	0.950	240.2 Da LogP -4.66 TPSA 158.7	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O…`
ZINC4353168	0.950	240.2 Da LogP -4.66 TPSA 158.7	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)…`
ZINC4353169	0.950	240.2 Da LogP -4.66 TPSA 158.7	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)…`
ZINC4353180	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O…`
ZINC4353181	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)…`
ZINC4353182	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)…`
ZINC95884213	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC9915770	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC9915771	0.950	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC100036265	0.857	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC100071552	0.857	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CO`
ZINC113074329	0.857	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC13522679	0.857	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC4353160	0.857	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)CO`
ZINC8579422	0.857	210.2 Da LogP -4.02 TPSA 138.5	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC57988531	0.600	360.3 Da LogP -6.60 TPSA 228.6	2 viol.	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@@H](O[C@@H](O)[C@H](O)[C…`
ZINC57988534	0.600	360.3 Da LogP -6.60 TPSA 228.6	2 viol.	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@H](O[C@@H](O)[C@H](O)[C@…`
ZINC2382315554	0.556	311.3 Da LogP -5.37 TPSA 201.8	1 viol.	✓ Clean	`N[C@@H](C=O)[C@@H](O)[C@H](O)[C@@H](O)C[C@H](O)…`
ZINC100055463	0.550	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	0.550	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	0.550	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	0.550	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	0.550	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	0.550	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	0.550	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	0.550	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	0.550	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	0.550	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	0.550	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`
ZINC253681754	0.538	247.3 Da LogP -0.63 TPSA 93.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H]1N[C@H](CO)[C@H](O)[C@@H](O)[C@@H]1O`
ZINC253681762	0.538	247.3 Da LogP -0.63 TPSA 93.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H]1N[C@H](CO)[C@H](O)[C@H](O)[C@H]1O`
ZINC253681766	0.538	247.3 Da LogP -0.63 TPSA 93.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H]1N[C@H](CO)[C@H](O)[C@H](O)[C@@H]1O`
ZINC253681771	0.538	247.3 Da LogP -0.63 TPSA 93.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H]1N[C@H](CO)[C@H](O)[C@@H](O)[C@H]1O`
ZINC4726346	0.538	225.2 Da LogP -4.73 TPSA 164.5	1 viol.	✓ Clean	`NC(=O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H…`
ZINC4726347	0.538	225.2 Da LogP -4.73 TPSA 164.5	1 viol.	✓ Clean	`NC(=O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H]…`
ZINC4726348	0.538	225.2 Da LogP -4.73 TPSA 164.5	1 viol.	✓ Clean	`NC(=O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H]…`
ZINC4726349	0.538	225.2 Da LogP -4.73 TPSA 164.5	1 viol.	✓ Clean	`NC(=O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](…`
ZINC1616450	0.536	254.3 Da LogP -1.28 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)[C@@H]1CCCN1)[C@@H]1CCCN1`
ZINC5203096	0.536	402.4 Da LogP -5.41 TPSA 214.4	2 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COC(=S)O…`
ZINC5203099	0.536	402.4 Da LogP -5.41 TPSA 214.4	2 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COC(=S)O…`
ZINC5600257	0.536	254.3 Da LogP -1.28 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)[C@H]1CCCN1)[C@H]1CCCN1`
ZINC8655607	0.536	254.3 Da LogP -1.28 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)[C@H]1CCCN1)[C@@H]1CCCN1`

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.