Protein profile

KP13_00143

Alpha-xylosidase

Genome: KpKP13

Gene: AHE42063.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GXH3

Export view

Amino acids 772

Annotations 6

Features 20

PDB binders 10

Druggability 0.212

Overview

Basic information about this protein and its source genome.

Accession: KP13_00143
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42063.1
Status: annotated
Amino acids: 772
Structure source: AlphaFold + ColabFold

3.2.1.177

GO:0030246 Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates. GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0004553 Catalysis of the hydrolysis of any O-glycosyl bond. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0061634 Catalysis of the hydrolysis of terminal, non-reducing alpha-D-xylose residues with release of alpha-D-xylose.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 29.535
Human E-value: 4.82e-41
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Unknown
ColabFold pLDDT: 97.96

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 0.212

Structure A0A0H3GXH3

Pocket Pocket 19

P2Rank 0.634

Structure A0A0H3GXH3

Pocket Pocket 1

ColabFold model

FPocket 0.179 · Pocket 21

P2Rank 0.586 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 280 / 4744 genomes with a hit

Normalized 0.059

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

3.2.1.177

Gene Ontology (GO)

GO:0030246 Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
GO:0004553 Catalysis of the hydrolysis of any O-glycosyl bond.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0061634 Catalysis of the hydrolysis of terminal, non-reducing alpha-D-xylose residues with release of alpha-D-xylose.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
263	603	SUPERFAMILY	SSF51445	(Trans)glycosidases
263	603	InterPro	IPR017853	Glycoside hydrolase superfamily
259	569	CDD	cd06593	GH31_xylosidase_YicI
666	772	SUPERFAMILY	SSF117125	Putative glucosidase YicI, C-terminal domain
617	664	Gene3D	G3DSA:2.60.40.1180	-
617	664	InterPro	IPR013780	Glycosyl hydrolase, all-beta
240	668	Pfam	PF01055	Glycosyl hydrolases family 31
240	668	InterPro	IPR000322	Glycoside hydrolase family 31
1	247	SUPERFAMILY	SSF74650	Galactose mutarotase-like
1	247	InterPro	IPR011013	Galactose mutarotase-like domain superfamily
28	664	PANTHER	PTHR43053	GLYCOSIDASE FAMILY 31
665	772	Gene3D	G3DSA:2.60.40.1180	-
665	772	InterPro	IPR013780	Glycosyl hydrolase, all-beta
246	616	FunFam	G3DSA:3.20.20.80:FF:000053	Alpha-xylosidase YicI
1	245	Gene3D	G3DSA:2.60.40.1760	glycosyl hydrolase (family 31)
586	665	SUPERFAMILY	SSF51011	Glycosyl hydrolase domain
150	259	CDD	cd14752	GH31_N
159	218	Pfam	PF13802	Galactose mutarotase-like
159	218	InterPro	IPR025887	Glycoside hydrolase family 31, N-terminal domain
246	616	Gene3D	G3DSA:3.20.20.80	Glycosidases

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...

Legend High Medium Low

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_A0A0H3GXH3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00143	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
19				0.212

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	10.57	0.568
2	4.55	0.195
3	2.76	0.084
4	2.38	0.063
5	1.74	0.031

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	9.35	0.502
2	2.58	0.074
3	2.31	0.059
4	2.28	0.057
5	1.95	0.041

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.

62 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
5GF	4BA0	B3PEE6	198.1 Da LogP -2.92 TPSA 110.4	✓ Ro5	✓ Clean	`C([C@@]1([C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O)F…`
66U	5I24	B3PEE6	193.2 Da LogP -3.62 TPSA 127.2	1 viol.	✓ Clean	`C([C@H]1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1O)O)O)…`
66V	5I23	B3PEE6	347.4 Da LogP -1.10 TPSA 163.5	1 viol.	Alert	`C(CCCCN=[N+]=N)CCCN[C@H]1[C@@H]([C@H]([C@@H]([C…`
93Z	5NPB	B3PEE6	274.2 Da LogP -3.76 TPSA 164.8	1 viol.	✓ Clean	`C([C@@H]1[C@H]([C@@H]([C@H](C([C@H]1OS(=O)(=O)O…`
948	5NPE	B3PEE6	175.2 Da LogP -2.97 TPSA 102.9	✓ Ro5	✓ Clean	`C([C@H]1[C@@H]2[C@@H](N2)[C@@H]([C@H]([C@@H]1O)…`
94B	5NPD	B3PEE6	175.2 Da LogP -2.97 TPSA 102.9	✓ Ro5	✓ Clean	`C([C@H]1[C@H]2[C@H](N2)[C@@H]([C@H]([C@@H]1O)O)…`
94E	5NPC	B3PEE6	256.2 Da LogP -3.28 TPSA 133.5	✓ Ro5	✓ Clean	`C([C@@H]1[C@H]([C@@H]([C@H]([C@@H]2[C@H]1OS(=O)…`
9VH	6PNR	C4ZGB7	211.2 Da LogP -2.18 TPSA 106.9	✓ Ro5	✓ Clean	`C1[C@@H]([C@H]([C@@H](CN1)O)O)CS(=O)(=O)O`
OXL	5NPB	B3PEE6	88.0 Da LogP -3.51 TPSA 80.3	✓ Ro5	✓ Clean	`C(=O)(C(=O)[O-])[O-]`
XTG	2F2H	P31434	449.4 Da LogP -2.05 TPSA 192.2	2 viol.	✓ Clean	`c1cc(ccc1[N+](=O)[O-])O[C@H]2[C@@H]([C@H]([C@@H…`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL408500	Q653V4	7.28	289.4 Da LogP 0.50 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCCCCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO`
CHEMBL179130	Q653V4	7.10	163.2 Da LogP -2.97 TPSA 93.0	✓ Ro5	✓ Clean	`OC[C@@H]1NC[C@@H](O)[C@@H](O)[C@H]1O`

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
ZINC14253608	1.000	289.4 Da LogP 0.50 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCCCCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO`
ZINC1552264	1.000	289.4 Da LogP 0.50 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCCCCCCN1C[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1CO`
ZINC44351037	1.000	331.5 Da LogP 1.67 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO`
ZINC3979739	0.967	233.3 Da LogP -1.06 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@@H]1CO`
ZINC11681341	0.871	219.3 Da LogP -1.45 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCN1C[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1CO`
ZINC13545227	0.871	219.3 Da LogP -1.45 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCN1C[C@@H](O)[C@@H](O)[C@H](O)[C@H]1CO`
ZINC13719785	0.871	219.3 Da LogP -1.45 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCN1C[C@H](O)[C@@H](O)[C@@H](O)[C@H]1CO`
ZINC1550969	0.871	219.3 Da LogP -1.45 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCN1C[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1CO`
ZINC2387141	0.871	219.3 Da LogP -1.45 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCN1C[C@H](O)[C@H](O)[C@@H](O)[C@@H]1CO`
ZINC36533584	0.871	219.3 Da LogP -1.45 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCN1C[C@H](O)[C@H](O)[C@H](O)[C@H]1CO`
ZINC3794711	0.871	219.3 Da LogP -1.45 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO`
ZINC3957104	0.871	219.3 Da LogP -1.45 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@@H]1CO`
ZINC71789999	0.871	219.3 Da LogP -1.45 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCN1C[C@H](O)[C@H](O)[C@@H](O)[C@H]1CO`
ZINC8627075	0.871	219.3 Da LogP -1.45 TPSA 84.2	✓ Ro5	✓ Clean	`CCCCN1C[C@H](O)[C@H](O)[C@H](O)[C@@H]1CO`
ZINC3825455	0.757	305.4 Da LogP -0.27 TPSA 93.4	✓ Ro5	✓ Clean	`CCCOCCCCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO`
ZINC253683038	0.750	205.3 Da LogP -1.84 TPSA 84.2	✓ Ro5	✓ Clean	`CCCN1C[C@H](O)[C@H](O)[C@@H](O)[C@@H]1CO`
ZINC253683042	0.750	205.3 Da LogP -1.84 TPSA 84.2	✓ Ro5	✓ Clean	`CCCN1C[C@H](O)[C@H](O)[C@H](O)[C@H]1CO`
ZINC253683044	0.750	205.3 Da LogP -1.84 TPSA 84.2	✓ Ro5	✓ Clean	`CCCN1C[C@H](O)[C@H](O)[C@@H](O)[C@H]1CO`
ZINC34383558	0.750	205.3 Da LogP -1.84 TPSA 84.2	✓ Ro5	✓ Clean	`CCCN1C[C@H](O)[C@H](O)[C@H](O)[C@@H]1CO`
ZINC137899614	0.722	319.4 Da LogP 0.12 TPSA 93.4	✓ Ro5	✓ Clean	`COCCCCCCCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO`
ZINC44960154	0.714	346.5 Da LogP 0.61 TPSA 110.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@@H]…`
ZINC44960155	0.714	346.5 Da LogP 0.61 TPSA 110.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCN1C[C@@H](O)[C@@H](O)[C@H](O)[C@@H…`
ZINC44960156	0.714	346.5 Da LogP 0.61 TPSA 110.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1…`
ZINC44960157	0.714	346.5 Da LogP 0.61 TPSA 110.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCN1C[C@@H](O)[C@@H](O)[C@H](O)[C@H]…`
ZINC95553643	0.692	333.5 Da LogP 0.25 TPSA 104.4	✓ Ro5	✓ Clean	`CCC(O)(CC)CCCCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@…`
ZINC22054059	0.676	277.3 Da LogP -1.61 TPSA 121.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCN1C[C@H](O)[C@H](O)[C@H](O)[C@H]1CO`
ZINC5157115	0.676	277.3 Da LogP -1.61 TPSA 121.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO`
ZINC6562433	0.676	277.3 Da LogP -1.61 TPSA 121.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCN1C[C@H](O)[C@H](O)[C@H](O)[C@@H]1CO`
ZINC6562434	0.676	277.3 Da LogP -1.61 TPSA 121.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@@H]1CO`
ZINC1070097	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@@H]2O[C@@H](CO)[C@@H](O)[…`
ZINC12359987	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@@H]2O[C@H](CO)[C@H](O)[C@…`
ZINC12359988	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@H]2O[C@H](CO)[C@H](O)[C@@…`
ZINC134307	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@H]2O[C@@H](CO)[C@H](O)[C@…`
ZINC134310	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@H]2O[C@@H](CO)[C@@H](O)[C…`
ZINC134325	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@@H]2O[C@@H](CO)[C@H](O)[C…`
ZINC156947	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@@H]2O[C@@H](CO)[C@@H](O)[…`
ZINC2539731	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@H]2O[C@@H](CO)[C@H](O)[C@…`
ZINC3956718	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@@H]2O[C@H](CO)[C@H](O)[C@…`
ZINC4028812	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@@H]2O[C@H](CO)[C@@H](O)[C…`
ZINC4282153	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@H]2O[C@H](CO)[C@@H](O)[C@…`
ZINC4282228	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@H]2O[C@H](CO)[C@@H](O)[C@…`
ZINC4282287	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@H]2O[C@H](CO)[C@H](O)[C@H…`
ZINC44963928	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@H]2O[C@H](CO)[C@H](O)[C@H…`
ZINC4521725	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@H]2O[C@@H](CO)[C@@H](O)[C…`
ZINC5227213	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@@H]2O[C@@H](CO)[C@@H](O)[…`
ZINC5227791	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@H]2O[C@H](CO)[C@H](O)[C@@…`
ZINC5842327	0.647	301.3 Da LogP -1.23 TPSA 142.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O[C@@H]2O[C@H](CO)[C@@H](O)[C…`
ZINC141935332	0.636	207.2 Da LogP -3.26 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN1C[C@H](O)[C@H](O)[C@@H](O)[C@H]1CO`
ZINC4097426	0.636	207.2 Da LogP -3.26 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN1C[C@H](O)[C@@H](O)[C@H](O)[C@H]1CO`
ZINC897171	0.636	207.2 Da LogP -3.26 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN1C[C@@H](O)[C@H](O)[C@@H](O)[C@@H]1CO`

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.