Protein profile

KP13_02024

5'-nucleotidase

Genome: KpKP13

Gene: AHE46460.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GM80

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Amino acids 225

Annotations 1

Features 24

PDB binders 6

Druggability 0.23

Overview

Basic information about this protein and its source genome.

Accession: KP13_02024
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46460.1
Status: annotated
Amino acids: 225
Structure source: AlphaFold + ColabFold

GO:0008253 Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 30.29
Human E-value: 6.95e-16
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 96.3

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 0.23

Structure A0A0H3GM80

Pocket Pocket 8

P2Rank 0.816

Structure A0A0H3GM80

Pocket Pocket 1

ColabFold model

FPocket 0.566 · Pocket 1

P2Rank 0.818 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 96 / 4744 genomes with a hit

Normalized 0.02

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

GO:0008253 Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
97	196	CDD	cd04305	HAD_Neu5Ac-Pase_like
5	218	Gene3D	G3DSA:3.40.50.1000	-
5	218	InterPro	IPR023214	HAD superfamily
92	195	NCBIfam	TIGR01509	HAD-IA family hydrolase
92	195	InterPro	IPR006439	HAD hydrolase, subfamily IA
4	221	NCBIfam	TIGR02254	noncanonical pyrimidine nucleotidase, YjjG family
4	221	InterPro	IPR011951	HAD-superfamily hydrolase, subfamily IA, YjjG/PynA
98	189	NCBIfam	TIGR01549	HAD-IA family hydrolase
98	189	InterPro	IPR006439	HAD hydrolase, subfamily IA
80	194	Pfam	PF13419	Haloacid dehalogenase-like hydrolase
80	194	InterPro	IPR041492	Haloacid dehalogenase-like hydrolase
137	153	PRINTS	PR00413	Haloacid dehalogenase/epoxide hydrolase family signature
137	153	InterPro	IPR006439	HAD hydrolase, subfamily IA
106	119	PRINTS	PR00413	Haloacid dehalogenase/epoxide hydrolase family signature
106	119	InterPro	IPR006439	HAD hydrolase, subfamily IA
184	197	PRINTS	PR00413	Haloacid dehalogenase/epoxide hydrolase family signature
184	197	InterPro	IPR006439	HAD hydrolase, subfamily IA
4	224	SFLD	SFLDG01135	C1.5.6: HAD, Beta-PGM, Phosphatase Like
16	95	Gene3D	G3DSA:1.10.150.240	Putative phosphatase; domain 2
16	95	InterPro	IPR023198	Phosphoglycolate phosphatase-like, domain 2
1	223	PANTHER	PTHR47478	-
4	224	SFLD	SFLDG01129	C1.5: HAD, Beta-PGM, Phosphatase Like
3	222	SUPERFAMILY	SSF56784	HAD-like
3	222	InterPro	IPR036412	HAD-like superfamily

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_A0A0H3GM80	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02024	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
8				0.23

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				14.65	0.729

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				0.566
10				0.334

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				15.75	0.761

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.

56 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
AC0	6Q7N	O58216	120.2 Da LogP 1.89 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccccc1`
BUA	1ZRM	Q53464	88.1 Da LogP 0.87 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC(=O)O`
LAC	1QH9	Q53464	90.1 Da LogP -0.55 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)O`
NHE	4YGR	B6YTD6	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCS(=O)(=O)O`
TBU	4YGQ	B6YTD6	74.1 Da LogP 0.78 TPSA 20.2	✓ Ro5	✓ Clean	`CC(C)(C)O`
VO4	4KNW	Q8TBE9	114.9 Da LogP -3.69 TPSA 86.2	✓ Ro5	✓ Clean	`[O-][V](=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
ZINC1710230	1.000	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC3200262	0.842	252.3 Da LogP 2.95 TPSA 51.2	✓ Ro5	Alert	`CC(=O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC36456728	0.800	224.3 Da LogP 3.12 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC2004372	0.786	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.786	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC1039926	0.625	220.3 Da LogP 3.29 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C#Cc2ccccc2)cc1`
ZINC143028	0.625	228.3 Da LogP 4.04 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(Sc2ccccc2)cc1`
ZINC1440490	0.625	222.3 Da LogP 4.06 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(/C=C/c2ccccc2)cc1`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC14981993	0.625	224.3 Da LogP 3.12 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1cccc(C(=O)c2ccccc2)c1`
ZINC1562037	0.625	210.3 Da LogP 3.48 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(Cc2ccccc2)cc1`
ZINC1675948	0.625	226.3 Da LogP 3.33 TPSA 41.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(NNc2ccccc2)cc1`
ZINC1845686	0.625	224.3 Da LogP 3.67 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(CCc2ccccc2)cc1`
ZINC21999250	0.625	211.3 Da LogP 3.63 TPSA 29.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(Nc2ccccc2)cc1`
ZINC261810	0.625	212.2 Da LogP 3.68 TPSA 26.3	✓ Ro5	✓ Clean	`CC(=O)c1ccc(Oc2ccccc2)cc1`
ZINC4798948	0.625	224.3 Da LogP 4.30 TPSA 41.8	✓ Ro5	Alert	`CC(=O)c1ccc(/N=N/c2ccccc2)cc1`
ZINC50452	0.615	240.3 Da LogP 3.11 TPSA 43.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(OC(=O)c2ccccc2)cc1`
ZINC586797	0.615	239.3 Da LogP 3.14 TPSA 46.2	✓ Ro5	✓ Clean	`CC(=O)c1ccc(NC(=O)c2ccccc2)cc1`
ZINC1672966	0.611	210.2 Da LogP 2.75 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1)c1ccccc1`
ZINC1401590	0.600	244.3 Da LogP 3.06 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc([S@](=O)c2ccccc2)cc1`
ZINC143035	0.600	260.3 Da LogP 2.72 TPSA 51.2	✓ Ro5	✓ Clean	`CC(=O)c1ccc(S(=O)(=O)c2ccccc2)cc1`
ZINC34354396	0.600	224.3 Da LogP 4.04 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc([C@@H](C)c2ccccc2)cc1`
ZINC34354398	0.600	224.3 Da LogP 4.04 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc([C@H](C)c2ccccc2)cc1`
ZINC4073660	0.600	244.3 Da LogP 3.06 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc([S@@](=O)c2ccccc2)cc1`
ZINC56557	0.600	238.3 Da LogP 3.76 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(-c2ccc(C(C)=O)cc2)cc1`
ZINC336592	0.583	224.3 Da LogP 3.12 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccccc1C(=O)c1ccccc1`
ZINC1529498	0.579	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1530417	0.579	228.4 Da LogP 4.77 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)O`
ZINC1577122	0.579	208.3 Da LogP 4.64 TPSA 0.0	✓ Ro5	✓ Clean	`C/C(=C(/C)c1ccccc1)c1ccccc1`
ZINC1590838	0.579	342.4 Da LogP 3.82 TPSA 68.3	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccccc2)cc1)c1ccccc1`
ZINC16133932	0.579	474.5 Da LogP 4.88 TPSA 102.4	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccc(C(=O)C(=O)c3cccc…`
ZINC1628119	0.579	214.3 Da LogP 4.38 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)O`
ZINC3123872	0.579	208.3 Da LogP 4.64 TPSA 0.0	✓ Ro5	✓ Clean	`C/C(=C(\C)c1ccccc1)c1ccccc1`
ZINC117551598	0.577	253.3 Da LogP 3.57 TPSA 37.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(N(C(C)=O)c2ccccc2)cc1`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC1556064	0.577	252.4 Da LogP 4.45 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(CCCCc2ccccc2)cc1`
ZINC1621063	0.577	268.3 Da LogP 2.82 TPSA 71.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C(=O)c2ccccc2C(=O)O)cc1`
ZINC1720928	0.577	238.3 Da LogP 4.06 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(CCCc2ccccc2)cc1`
ZINC2039629	0.577	222.3 Da LogP 4.06 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1cccc(/C=C/c2ccccc2)c1`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC47679	0.577	254.3 Da LogP 3.53 TPSA 58.2	✓ Ro5	✓ Clean	`CC(=O)c1ccc(NC(=O)Nc2ccccc2)cc1`
ZINC1604259	0.571	346.3 Da LogP 4.99 TPSA 51.2	✓ Ro5	✓ Clean	`O=C(c1ccccc1)P(C(=O)c1ccccc1)C(=O)c1ccccc1`
ZINC2113934064	0.571	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCCCCCCC(=O)O`
ZINC2113934089	0.571	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2378809	0.571	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCC(=O)O`
ZINC5613445	0.571	240.3 Da LogP 2.06 TPSA 38.0	✓ Ro5	✓ Clean	`CC(=O)c1cc[n+](CC(=O)c2ccccc2)cc1`

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.