Protein profile

KP13_04481

Pyrimidine-specific ribonucleoside hydrolase rihA

Genome: KpKP13

Gene: rihA AHE44354.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTH3

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Amino acids 311

Annotations 8

Features 14

PDB binders 6

Druggability 0.662

Overview

Basic information about this protein and its source genome.

Accession: KP13_04481
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rihA AHE44354.1
Status: annotated
Amino acids: 311
Structure source: AlphaFold + ColabFold

3.2.-.-

GO:0006206 The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases. GO:0045437 Catalysis of the reaction: H2O + uridine = ribofuranose + uracil. GO:0016799 Catalysis of the hydrolysis of any N-glycosyl bond. GO:0015949 The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0008477 Catalysis of the reaction: a N-D-ribosylpurine + H2O = a purine + D-ribose.

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 (%): 42.395
DEG E-value: 3.2799999999999995e-67
Localization: Unknown
ColabFold pLDDT: 97.78

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 0.662

Structure A0A0H3GTH3

Pocket Pocket 1

P2Rank 0.842

Structure A0A0H3GTH3

Pocket Pocket 1

ColabFold model

FPocket 0.804 · Pocket 1

P2Rank 0.822 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 145 / 4744 genomes with a hit

Normalized 0.031

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

3.2.-.-

Gene Ontology (GO)

GO:0006206 The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
GO:0045437 Catalysis of the reaction: H2O + uridine = ribofuranose + uracil.
GO:0016799 Catalysis of the hydrolysis of any N-glycosyl bond.
GO:0015949 The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0008477 Catalysis of the reaction: a N-D-ribosylpurine + H2O = a purine + D-ribose.
GO:0006152 The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
1	311	Hamap	MF_01431	Pyrimidine-specific ribonucleoside hydrolase RihA [rihA].
1	311	InterPro	IPR022975	Pyrimidine-specific ribonucleoside hydrolase RihA
1	311	Gene3D	G3DSA:3.90.245.10	-
1	311	InterPro	IPR036452	Ribonucleoside hydrolase-like
1	311	FunFam	G3DSA:3.90.245.10:FF:000001	Pyrimidine-specific ribonucleoside hydrolase RihA
8	18	ProSitePatterns	PS01247	Inosine-uridine preferring nucleoside hydrolase family signature.
8	18	InterPro	IPR015910	Inosine/uridine-preferring nucleoside hydrolase, conserved site
4	307	CDD	cd02651	nuc_hydro_IU_UC_XIUA
5	308	PANTHER	PTHR12304	INOSINE-URIDINE PREFERRING NUCLEOSIDE HYDROLASE
5	308	InterPro	IPR023186	Inosine/uridine-preferring nucleoside hydrolase
4	307	SUPERFAMILY	SSF53590	Nucleoside hydrolase
4	307	InterPro	IPR036452	Ribonucleoside hydrolase-like
5	301	Pfam	PF01156	Inosine-uridine preferring nucleoside hydrolase
5	301	InterPro	IPR001910	Inosine/uridine-preferring nucleoside hydrolase domain

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_A0A0H3GTH3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04481	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
1				0.662
2				0.44

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				16.48	0.779
2				0.74	0.002

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				0.804

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				15.69	0.759

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.

57 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
ADE	6ZK4	B6THD4	135.1 Da LogP -0.06 TPSA 80.5	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)c(ncn2)N`
DNB	3MKN	C3T3U2	239.3 Da LogP -1.42 TPSA 124.8	1 viol.	✓ Clean	`c1cc(c(cc1[C@H]2[C@@H]([C@@H]([C@H](N2)CO)O)O)N…`
IMH	6ZK2	B6THD4	266.3 Da LogP -2.02 TPSA 134.3	1 viol.	✓ Clean	`c1c(c2c([nH]1)C(=O)NC=N2)[C@H]3[C@@H]([C@@H]([C…`
NOS	3B9X	P33022	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=…`
PIR	2MAS	Q27546	224.3 Da LogP -1.00 TPSA 98.7	✓ Ro5	✓ Clean	`c1cc(ccc1[C@H]2[C@@H]([C@@H]([C@H](N2)CO)O)O)N`
TAM	3B9X	P33022	163.2 Da LogP -1.17 TPSA 86.7	✓ Ro5	✓ Clean	`C(CO)C(CCO)(CCO)N`

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
CHEMBL3827395	Q27546	8.15	265.3 Da LogP -2.09 TPSA 136.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1N=CC2[C@@H]1N[C@H](CO)[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
ZINC13492899	1.000	266.3 Da LogP -2.02 TPSA 134.3	1 viol.	✓ Clean	`O=c1[nH]cnc2c([C@@H]3N[C@H](CO)[C@@H](O)[C@H]3O…`
ZINC104646465	0.750	298.3 Da LogP -0.90 TPSA 113.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(=O)[nH]cnc32)[C@H](O)[…`
ZINC104896921	0.750	298.3 Da LogP -0.90 TPSA 113.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(=O)[nH]cnc32)[C@@H](O)…`
ZINC13508805	0.750	298.3 Da LogP -0.90 TPSA 113.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]cnc32)[C@@H](O…`
ZINC13508807	0.750	298.3 Da LogP -0.90 TPSA 113.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@@H](n2cnc3c(=O)[nH]cnc32)[C@@H](O)…`
ZINC13508809	0.750	298.3 Da LogP -0.90 TPSA 113.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(=O)[nH]cnc32)[C@@H](O)…`
ZINC225456440	0.750	282.3 Da LogP -1.61 TPSA 122.5	✓ Ro5	✓ Clean	`COC[C@@H]1O[C@H](n2cnc3c(=O)[nH]cnc32)[C@H](O)[…`
ZINC230149202	0.750	282.3 Da LogP -1.61 TPSA 122.5	✓ Ro5	✓ Clean	`COC[C@@H]1O[C@H](n2cnc3c(=O)[nH]cnc32)[C@@H](O)…`
ZINC28542039	0.750	298.3 Da LogP -0.90 TPSA 113.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@@H](n2cnc3c(=O)[nH]cnc32)[C@@H](O)…`
ZINC34328902	0.750	298.3 Da LogP -0.90 TPSA 113.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]cnc32)[C@@H](O…`
ZINC8652317	0.745	312.4 Da LogP -0.51 TPSA 113.3	✓ Ro5	✓ Clean	`CCS[C@@H]1[C@@H](O)[C@H](CO)O[C@@H]1n1cnc2c(=O)…`
ZINC16382907	0.739	284.3 Da LogP -0.90 TPSA 116.4	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](n2cnc3c(=S)[nH]cnc32)[C@@H](O)[…`
ZINC16382910	0.739	284.3 Da LogP -0.90 TPSA 116.4	✓ Ro5	✓ Clean	`OC[C@H]1O[C@H](n2cnc3c(=S)[nH]cnc32)[C@@H](O)[C…`
ZINC2158	0.739	284.3 Da LogP -0.90 TPSA 116.4	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@H](n2cnc3c(=S)[nH]cnc32)[C@@H](O)[…`
ZINC3148526	0.739	284.3 Da LogP -0.90 TPSA 116.4	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@H](n2cnc3c(=S)[nH]cnc32)[C@H](O)[C…`
ZINC4217548	0.739	284.3 Da LogP -0.90 TPSA 116.4	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](n2cnc3c(=S)[nH]cnc32)[C@H](O)[C…`
ZINC5510729	0.739	284.3 Da LogP -0.90 TPSA 116.4	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@H](n2cnc3c(=S)[nH]cnc32)[C@H](O)[C…`
ZINC5510732	0.739	284.3 Da LogP -0.90 TPSA 116.4	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@H](n2cnc3c(=S)[nH]cnc32)[C@@H](O)[…`
ZINC5510735	0.739	284.3 Da LogP -0.90 TPSA 116.4	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@@H](n2cnc3c(=S)[nH]cnc32)[C@H](O)[…`
ZINC5510738	0.739	284.3 Da LogP -0.90 TPSA 116.4	✓ Ro5	✓ Clean	`OC[C@@H]1O[C@@H](n2cnc3c(=S)[nH]cnc32)[C@@H](O)…`
ZINC65743212	0.739	284.3 Da LogP -0.90 TPSA 116.4	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](n2cnc3c(=S)[nH]cnc32)[C@@H](O)[…`
ZINC80121649	0.739	284.3 Da LogP -0.90 TPSA 116.4	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](n2cnc3c(=S)[nH]cnc32)[C@H](O)[C…`
ZINC14951284	0.706	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C…`
ZINC1532551	0.706	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@…`
ZINC16969369	0.706	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@…`
ZINC4228242	0.706	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@…`
ZINC4353761	0.706	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C…`
ZINC8614392	0.706	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C…`
ZINC16926920	0.702	282.3 Da LogP -1.88 TPSA 133.5	✓ Ro5	✓ Clean	`C[C@@H]1O[C@@H](n2cnc3c(=O)[nH]cnc32)[C@@H](O)[…`
ZINC16926924	0.702	282.3 Da LogP -1.88 TPSA 133.5	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(=O)[nH]cnc32)[C@@H](O)[C…`
ZINC4876777	0.702	282.3 Da LogP -1.88 TPSA 133.5	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2cnc3c(=O)[nH]cnc32)[C@@H](O)[C…`
ZINC4876778	0.702	282.3 Da LogP -1.88 TPSA 133.5	✓ Ro5	✓ Clean	`C[C@@H]1O[C@@H](n2cnc3c(=O)[nH]cnc32)[C@@H](O)[…`
ZINC1532637	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](O)[C@@H]2O)c…`
ZINC1550030	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c…`
ZINC1570863	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(…`
ZINC1698205	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c…`
ZINC2020098	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c(…`
ZINC3869967	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c…`
ZINC3869968	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)…`
ZINC3869969	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)…`
ZINC3869970	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O…`
ZINC5605239	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c…`
ZINC6119283	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)c(…`
ZINC6585367	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)…`
ZINC8613125	0.694	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c…`
ZINC12655466	0.686	308.3 Da LogP -0.47 TPSA 111.5	✓ Ro5	✓ Clean	`CC1(C)O[C@H]2[C@H](O1)[C@@H](CO)O[C@H]2n1cnc2c(…`
ZINC15277561	0.686	308.3 Da LogP -0.47 TPSA 111.5	✓ Ro5	✓ Clean	`CC1(C)O[C@H]2[C@@H](CO)O[C@@H](n3cnc4c(=O)[nH]c…`
ZINC15277563	0.686	308.3 Da LogP -0.47 TPSA 111.5	✓ Ro5	✓ Clean	`CC1(C)O[C@@H]2[C@H](CO)O[C@@H](n3cnc4c(=O)[nH]c…`
ZINC8892889	0.686	308.3 Da LogP -0.47 TPSA 111.5	✓ Ro5	✓ Clean	`CC1(C)O[C@H]2[C@H](CO)O[C@H](n3cnc4c(=O)[nH]cnc…`
ZINC8955192	0.686	308.3 Da LogP -0.47 TPSA 111.5	✓ Ro5	✓ Clean	`CC1(C)O[C@H]2[C@@H](CO)O[C@H](n3cnc4c(=O)[nH]cn…`

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.