Protein profile

KP13_04769

AMP nucleosidase

Genome: KpKP13

Gene: AHE43732.1 amn Structure source: Experimental + ColabFold UniProt W9BAW3

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Amino acids 484

Annotations 6

Features 18

PDB binders 1

Druggability 0.712

Overview

Basic information about this protein and its source genome.

Accession: KP13_04769
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43732.1 amn
Status: annotated
Amino acids: 484
Structure source: Experimental + ColabFold

3.2.2.4

GO:0044209 The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis. GO:0009116 The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine). 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:0008714 Catalysis of the reaction: AMP + H2O = D-ribose 5-phosphate + adenine. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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: 92.77

Selected Druggability evidence

PDB experimental structure

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 0.712

Structure 7UWQ

Pocket Pocket 1

P2Rank 0.498

Structure 7UWQ

Pocket Pocket 1

ColabFold model

FPocket 0.601 · Pocket 3

P2Rank 0.754 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 113 / 4744 genomes with a hit

Normalized 0.024

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)

3.2.2.4

Gene Ontology (GO)

GO:0044209 The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
GO:0009116 The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
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:0008714 Catalysis of the reaction: AMP + H2O = D-ribose 5-phosphate + adenine.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
173	484	Gene3D	G3DSA:3.40.50.1580	Nucleoside phosphorylase domain
173	484	InterPro	IPR035994	Nucleoside phosphorylase superfamily
12	167	Pfam	PF10423	Bacterial AMP nucleoside phosphorylase N-terminus
12	167	InterPro	IPR018953	AMP nucleoside phosphorylase, N-terminal
266	431	Pfam	PF01048	Phosphorylase superfamily
266	431	InterPro	IPR000845	Nucleoside phosphorylase domain
10	484	NCBIfam	TIGR01717	AMP nucleosidase
10	484	InterPro	IPR011271	AMP nucleosidase
9	484	SUPERFAMILY	SSF53167	Purine and uridine phosphorylases
9	484	InterPro	IPR035994	Nucleoside phosphorylase superfamily
175	461	PANTHER	PTHR43691	URIDINE PHOSPHORYLASE
173	484	FunFam	G3DSA:3.40.50.1580:FF:000005	AMP nucleosidase
178	462	CDD	cd17762	AMN
178	462	InterPro	IPR047039	AMP nucleosidase, phosphorylase domain
3	484	Hamap	MF_01932	AMP nucleosidase [amn].
3	484	InterPro	IPR011271	AMP nucleosidase
1	172	Gene3D	G3DSA:3.30.1730.10	-
1	172	InterPro	IPR037109	AMP nucleoside phosphorylase, N-terminal domain 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

1 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 7UWQ	X-ray	20.00 Å	-	—	PDBe RCSB PDBj File	Viewing
ColabFold KP13_04769	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
200				0.461
188				0.335
210				0.278
216				0.24

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	15.78	0.762
2	14.56	0.726
3	13.42	0.685
4	13.29	0.681
5	13.09	0.674

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
3				0.601
1				0.234

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	12.43	0.65
2	6.46	0.326
3	4.49	0.192
4	3.71	0.141
5	2.01	0.044

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.

32 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
FMP	1T8S	P0AE12	347.2 Da LogP -1.79 TPSA 196.9	1 viol.	✓ Clean	`c1nc2c(c(n1)N)[nH]nc2[C@H]3[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).

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
ZINC32138281	0.590	384.4 Da LogP -1.37 TPSA 193.5	1 viol.	✓ Clean	`Nc1ncnc2c([C@@H]3O[C@H](CSCC[C@H](N)C(=O)O)[C@@…`
ZINC8577182	0.536	268.2 Da LogP -1.79 TPSA 144.6	✓ Ro5	✓ Clean	`OC[C@H]1O[C@@H](c2n[nH]c3c(O)ncnc23)[C@H](O)[C@…`
ZINC4972228	0.534	310.3 Da LogP -1.30 TPSA 124.4	✓ Ro5	✓ Clean	`C[N+](C)(C)c1ncnc2c([C@H]3O[C@@H](CO)[C@@H](O)[…`
ZINC8628081	0.525	282.3 Da LogP -2.21 TPSA 162.4	1 viol.	✓ Clean	`NNc1ncnc2c([C@H]3O[C@@H](CO)[C@@H](O)[C@H]3O)n[…`
ZINC8628082	0.525	282.3 Da LogP -2.21 TPSA 162.4	1 viol.	✓ Clean	`NNc1ncnc2c([C@@H]3O[C@@H](CO)[C@@H](O)[C@H]3O)n…`
ZINC13518964	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.525	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8638190	0.508	283.2 Da LogP -1.69 TPSA 156.6	1 viol.	✓ Clean	`OC[C@@H]1O[C@H](c2n[nH]c3c(NO)ncnc23)[C@H](O)[C…`
ZINC8638192	0.508	283.2 Da LogP -1.69 TPSA 156.6	1 viol.	✓ Clean	`OC[C@@H]1O[C@@H](c2n[nH]c3c(NO)ncnc23)[C@H](O)[…`
ZINC8638194	0.508	283.2 Da LogP -1.69 TPSA 156.6	1 viol.	✓ Clean	`OC[C@@H]1O[C@H](c2n[nH]c3c(NO)ncnc23)[C@@H](O)[…`
ZINC8638195	0.508	283.2 Da LogP -1.69 TPSA 156.6	1 viol.	✓ Clean	`OC[C@@H]1O[C@@H](c2n[nH]c3c(NO)ncnc23)[C@@H](O)…`
ZINC4830848	0.500	283.2 Da LogP -2.67 TPSA 164.5	✓ Ro5	✓ Clean	`Nc1c2[nH]nc([C@H]3O[C@@H](CO)[C@@H](O)[C@H]3O)c…`
ZINC4830849	0.500	283.2 Da LogP -2.67 TPSA 164.5	✓ Ro5	✓ Clean	`Nc1c2[nH]nc([C@@H]3O[C@@H](CO)[C@@H](O)[C@H]3O)…`
ZINC4830850	0.500	283.2 Da LogP -2.67 TPSA 164.5	✓ Ro5	✓ Clean	`Nc1c2[nH]nc([C@H]3O[C@@H](CO)[C@@H](O)[C@@H]3O)…`
ZINC4830852	0.500	283.2 Da LogP -2.67 TPSA 164.5	✓ Ro5	✓ Clean	`Nc1c2[nH]nc([C@@H]3O[C@@H](CO)[C@@H](O)[C@@H]3O…`
ZINC5424976	0.500	298.3 Da LogP -0.77 TPSA 124.4	✓ Ro5	✓ Clean	`CSc1ncnc2c([C@@H]3O[C@@H](CO)[C@@H](O)[C@@H]3O)…`
ZINC8659460	0.500	324.2 Da LogP -2.83 TPSA 201.1	1 viol.	✓ Clean	`NC(=O)c1n[nH]c([C@@H]2O[C@H](COP(=O)(O)O)[C@H](…`
ZINC8659461	0.500	324.2 Da LogP -2.83 TPSA 201.1	1 viol.	✓ Clean	`NC(=O)c1n[nH]c([C@@H]2O[C@@H](COP(=O)(O)O)[C@H]…`
ZINC8659462	0.500	324.2 Da LogP -2.83 TPSA 201.1	1 viol.	✓ Clean	`NC(=O)c1n[nH]c([C@@H]2O[C@H](COP(=O)(O)O)[C@@H]…`
ZINC8659463	0.500	324.2 Da LogP -2.83 TPSA 201.1	1 viol.	✓ Clean	`NC(=O)c1n[nH]c([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H…`

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.