Protein profile

KP13_02913

Xanthine phosphoribosyltransferase

Genome: KpKP13

Gene: AHE46190.1 gpt Structure source: AlphaFold + ColabFold UniProt A0A0H3GSB1

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Amino acids 152

Annotations 11

Features 13

PDB binders 15

Druggability 0.257

Overview

Basic information about this protein and its source genome.

Accession: KP13_02913
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46190.1 gpt
Status: annotated
Amino acids: 152
Structure source: AlphaFold + ColabFold

2.4.2.22

GO:0000310 Catalysis of the reaction: diphosphate + XMP = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0052657 Catalysis of the reaction: GMP + diphosphate = guanine + 5-phospho-alpha-D-ribose 1-diphosphate. GO:0004422 Catalysis of the reaction: IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate. GO:0000287 Binding to a magnesium (Mg) ion.

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 (%): 72.258
DEG E-value: 1.71e-82
Localization: Cytoplasmic
ColabFold pLDDT: 94.72

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 0.257

Structure A0A0H3GSB1

Pocket Pocket 9

P2Rank 0.229

Structure A0A0H3GSB1

Pocket Pocket 1

ColabFold model

FPocket 0.278 · Pocket 11

P2Rank 0.392 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 168 / 4744 genomes with a hit

Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

2.4.2.22

Gene Ontology (GO)

GO:0000310 Catalysis of the reaction: diphosphate + XMP = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0052657 Catalysis of the reaction: GMP + diphosphate = guanine + 5-phospho-alpha-D-ribose 1-diphosphate.
GO:0004422 Catalysis of the reaction: IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate.
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0032263 Any process which produces guanosine monophosphate from derivatives of it, without de novo synthesis.
GO:0032264 Any process which produces inosine monophosphate from derivatives of it, without de novo synthesis.
GO:0006166 Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
GO:0032265 Any process which produces xanthosine monophosphate from derivatives of it, without de novo synthesis.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
32	129	CDD	cd06223	PRTases_typeI
32	129	InterPro	IPR000836	Phosphoribosyltransferase domain
1	152	Gene3D	G3DSA:3.40.50.2020	-
1	152	InterPro	IPR029057	Phosphoribosyltransferase-like
12	144	Pfam	PF00156	Phosphoribosyl transferase domain
12	144	InterPro	IPR000836	Phosphoribosyltransferase domain
4	144	SUPERFAMILY	SSF53271	PRTase-like
4	144	InterPro	IPR029057	Phosphoribosyltransferase-like
1	152	FunFam	G3DSA:3.40.50.2020:FF:000009	Xanthine phosphoribosyltransferase
1	152	Hamap	MF_01903	Xanthine-guanine phosphoribosyltransferase [gpt].
1	152	InterPro	IPR023747	Xanthine-guanine phosphoribosyltransferase
1	151	PANTHER	PTHR39563	XANTHINE PHOSPHORIBOSYLTRANSFERASE
1	151	InterPro	IPR023747	Xanthine-guanine phosphoribosyltransferase

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_A0A0H3GSB1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02913	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
9				0.257

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				2.18	0.052
2				1.73	0.031

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
11				0.278

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				2.83	0.088
2				2.2	0.053

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.

67 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
3L5	5KNR	P0A9M2	454.3 Da LogP -1.62 TPSA 217.1	1 viol.	✓ Clean	`c1nc2c(n1CCN(CCOCCP(=O)(O)O)CCP(=O)(O)O)NC(=NC2…`
3L7	5KNS	P0A9M2	437.3 Da LogP -0.74 TPSA 191.1	✓ Ro5	✓ Clean	`c1nc2c(n1CCN(CCO/C=C/P(=O)(O)O)CCP(=O)(O)O)N=CN…`
3ZE	4JLS	P0A9M5	358.3 Da LogP -2.38 TPSA 187.7	✓ Ro5	✓ Clean	`c1nc2c(n1[C@H]3CN(C[C@H]3O)C(=O)CP(=O)(O)O)N=C(…`
3ZF	4JIT	P0A9M5	342.3 Da LogP -1.35 TPSA 167.4	✓ Ro5	✓ Clean	`c1nc2c(n1[C@H]3CCN(C3)C(=O)CP(=O)(O)O)N=C(NC2=O…`
5GP	1A97	P0A9M5	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…`
6W9	5KNV	P0A9M2	423.3 Da LogP -0.44 TPSA 181.9	✓ Ro5	✓ Clean	`c1nc2c(n1CCN(CCCCP(=O)(O)O)CCP(=O)(O)O)N=CNC2=O`
6WA	5KNU	P0A9M2	408.3 Da LogP 0.19 TPSA 179.8	1 viol.	✓ Clean	`c1c(c2c([nH]1)C(=O)NC=N2)CN(CCCP(=O)(O)O)CCCP(=…`
6WB	5KNT	P0A9M2	361.3 Da LogP -2.05 TPSA 164.8	✓ Ro5	✓ Clean	`c1nc2c(n1CCN(CCP(=O)(O)O)C[C@@H](CO)O)N=CNC2=O`
6WC	5KNX	P0A9M2	412.2 Da LogP -0.96 TPSA 197.1	✓ Ro5	✓ Clean	`c1nc2c(n1CC(COCP(=O)(O)O)COCP(=O)(O)O)N=CNC2=O`
ADE	4TRC	Q97W95	135.1 Da LogP -0.06 TPSA 80.5	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)c(ncn2)N`
BO3	1A95	P0A9M5	61.8 Da LogP -2.05 TPSA 60.7	✓ Ro5	✓ Clean	`B(O)(O)O`
GUN	1A95	P0A9M5	151.1 Da LogP -0.77 TPSA 100.5	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)C(=O)NC(=N2)N`
IMP	1G9S	P0A9M2	348.2 Da LogP -2.15 TPSA 180.0	✓ Ro5	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…`
PCP	1A95	P0A9M5	388.1 Da LogP -1.57 TPSA 220.5	1 viol.	✓ Clean	`C1[C@@H]([C@H]([C@H]([C@H]1O[P@](=O)(O)OP(=O)(O…`
XAN	1A96	P0A9M5	152.1 Da LogP -1.06 TPSA 94.4	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)C(=O)NC(=O)N2`

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
CHEMBL3897903	P0A9M5	6.40	440.3 Da LogP -1.67 TPSA 217.1	1 viol.	✓ Clean	`Nc1nc2c(ncn2CCN(CCOCP(=O)(O)O)CCP(=O)(O)O)c(=O)…`
CHEMBL5565343	P0A9M5	6.00	494.3 Da LogP -1.39 TPSA 234.2	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](COCCP(=O)(O)O)N(C(=O)…`

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
ZINC12501413	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC12958448	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC1532555	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC16546189	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC2159505	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3073318	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869963	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869965	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC9334496	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC104869865	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…`
ZINC12504289	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC34541308	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC35000839	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC45284491	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC80639694	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC8215481	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC33979258	0.800	364.2 Da LogP -2.45 TPSA 200.2	1 viol.	✓ Clean	`O=c1[nH]c(O)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)…`
ZINC33979259	0.800	364.2 Da LogP -2.45 TPSA 200.2	1 viol.	✓ Clean	`O=c1[nH]c(O)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)…`
ZINC78920152	0.800	364.2 Da LogP -2.45 TPSA 200.2	1 viol.	✓ Clean	`O=c1[nH]c(O)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)…`
ZINC71774763	0.758	432.3 Da LogP -2.23 TPSA 198.3	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@](=O)(O)N3CCOCC3…`
ZINC1532183	0.745	289.2 Da LogP -1.15 TPSA 156.3	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2CCOCP(=O)(O)O)c(=O)[nH]1`
ZINC12296728	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)…`
ZINC13527599	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O…`
ZINC13527603	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)…`
ZINC1532627	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)…`
ZINC1730395	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O…`
ZINC3869846	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O…`
ZINC3869847	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2…`
ZINC3869848	0.741	347.2 Da LogP -1.54 TPSA 185.8	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O…`
ZINC4743771	0.741	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC4743772	0.741	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC4743774	0.741	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC4743775	0.741	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC14951284	0.732	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	0.732	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	0.732	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	0.732	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	0.732	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	0.732	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…`
ZINC12503440	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC1530370	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](OP(=O)(O)O)[…`
ZINC28631009	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](OP(=O)(O)O)[…`
ZINC3872740	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC3872741	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…`
ZINC3872742	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC3872743	0.729	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…`
ZINC1532637	0.722	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…`
ZINC4990799	0.722	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(=O)[nH]c(N)nc32)[C@H](O…`
ZINC6119283	0.722	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	0.722	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)…`

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.