Protein profile

KP13_03836

GDP-mannose pyrophosphatase nudK

Genome: KpKP13

Gene: AHE43320.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GRI0

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Amino acids 198

Annotations 5

Features 12

PDB binders 7

Druggability 0.323

Overview

Basic information about this protein and its source genome.

Accession: KP13_03836
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43320.1
Status: annotated
Amino acids: 198
Structure source: AlphaFold + ColabFold

GO:0016818 Catalysis of the hydrolysis of any acid anhydride which contains phosphorus. GO:0046872 Binding to a metal ion. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0006753 The chemical reactions and pathways involving any phosphorylated nucleoside. GO:0019693 The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 32.37
Human E-value: 1.07e-08
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 95.18

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 0.323

Structure A0A0H3GRI0

Pocket Pocket 9

P2Rank 0.184

Structure A0A0H3GRI0

Pocket Pocket 1

ColabFold model

FPocket 0.01 · Pocket 3

P2Rank 0.304 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 111 / 4744 genomes with a hit

Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0016818 Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
GO:0046872 Binding to a metal ion.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0006753 The chemical reactions and pathways involving any phosphorylated nucleoside.
GO:0019693 The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
44	185	CDD	cd03424	ADPRase_NUDT5
2	190	Gene3D	G3DSA:3.90.79.10	Nucleoside Triphosphate Pyrophosphohydrolase
17	184	PANTHER	PTHR11839	UDP/ADP-SUGAR PYROPHOSPHATASE
1	191	FunFam	G3DSA:3.90.79.10:FF:000010	GDP-mannose pyrophosphatase NudK
43	180	ProSiteProfiles	PS51462	Nudix hydrolase domain profile.
43	180	InterPro	IPR000086	NUDIX hydrolase domain
11	186	SUPERFAMILY	SSF55811	Nudix
11	186	InterPro	IPR015797	NUDIX hydrolase-like domain superfamily
7	186	NCBIfam	TIGR00052	nudix-type nucleoside diphosphatase, YffH/AdpP family
7	186	InterPro	IPR004385	Nucleoside diphosphate pyrophosphatase
45	163	Pfam	PF00293	NUDIX domain
45	163	InterPro	IPR000086	NUDIX 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_A0A0H3GRI0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03836	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				0.323
1				0.314

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				2.91	0.093
2				1.44	0.019

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				3.77	0.145
2				1.61	0.026

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
ADV	1KHZ	Q93K97	557.3 Da LogP -3.17 TPSA 282.3	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
APR	1V8L	Q84CU3	559.3 Da LogP -3.28 TPSA 291.5	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
AR6	3X0K	Q5SKW5	559.3 Da LogP -3.28 TPSA 291.5	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
GD3	1GA7	Q93K97	157.2 Da LogP 0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Gd+3]`
GDD	3O61	P37128	605.3 Da LogP -4.63 TPSA 331.7	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…`
R5P	1V8T	Q84CU3	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`C(C(C(C(C=O)O)O)O)OP(=O)(O)O`
TAR	3O52	P37128	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@H]([C@@H](C(=O)O)O)(C(=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
ZINC1530556	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC22116391	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC3606137	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC3869426	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC8551307	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC8551308	1.000	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC100033330	0.889	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC100067275	0.889	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC100889630	0.889	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC104861723	0.889	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O…`
ZINC12503760	0.889	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC12503763	0.889	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC19850142	0.889	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC2508229	0.889	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4545927	0.889	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COP(=O)(…`
ZINC4545928	0.889	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O…`
ZINC4545929	0.889	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)COP(=O)(O…`
ZINC12360002	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC13518964	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.782	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	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.782	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	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.782	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	0.782	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	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC1532601	0.778	200.1 Da LogP -1.98 TPSA 124.3	✓ Ro5	✓ Clean	`O=C[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC32786787	0.778	200.1 Da LogP -1.98 TPSA 124.3	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4096224	0.768	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC12503850	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141161066	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC12504289	0.761	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)(…`
ZINC105372833	0.750	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`

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.