Protein profile

KP13_05660

Pyrazinamidase/nicotinamidase

Genome: KpKP13

Gene: AHE45068.1 pncA Structure source: AlphaFold + ColabFold UniProt A0A0H3GRH4

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Amino acids 213

Annotations 4

Features 9

PDB binders 2

Druggability 0.45

Overview

Basic information about this protein and its source genome.

Accession: KP13_05660
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45068.1 pncA
Status: annotated
Amino acids: 213
Structure source: AlphaFold + ColabFold

3.5.1.19

GO:0046872 Binding to a metal ion. GO:0008936 Catalysis of the reaction: nicotinamide + H2O = nicotinate + NH4+. GO:0019363 The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.

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: 97.46

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 0.45

Structure A0A0H3GRH4

Pocket Pocket 2

P2Rank 0.387

Structure A0A0H3GRH4

Pocket Pocket 1

ColabFold model

FPocket 0.486 · Pocket 2

P2Rank 0.417 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 118 / 4744 genomes with a hit

Normalized 0.025

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

3.5.1.19

Gene Ontology (GO)

GO:0046872 Binding to a metal ion.
GO:0008936 Catalysis of the reaction: nicotinamide + H2O = nicotinate + NH4+.
GO:0019363 The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.

Sequence Features

Domain/signature hits from InterPro and related databases.

9 records

Show feature table

Start	End	DB	Term	Name
3	203	Gene3D	G3DSA:3.40.50.850	-
3	203	InterPro	IPR036380	Isochorismatase-like superfamily
3	206	PANTHER	PTHR11080	PYRAZINAMIDASE/NICOTINAMIDASE
5	206	Pfam	PF00857	Isochorismatase family
5	206	InterPro	IPR000868	Isochorismatase-like
3	208	FunFam	G3DSA:3.40.50.850:FF:000006	Bifunctional pyrazinamidase/nicotinamidase
2	209	SUPERFAMILY	SSF52499	Isochorismatase-like hydrolases
2	209	InterPro	IPR036380	Isochorismatase-like superfamily
4	202	CDD	cd01011	nicotinamidase

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_A0A0H3GRH4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05660	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
2				0.45

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				6.43	0.324
2				1.56	0.024

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
2				0.486

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				7.31	0.381

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.

52 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
NH4	3HB7	A6TWT6	18.0 Da LogP 0.38 TPSA 36.5	✓ Ro5	✓ Clean	`[NH4+]`
NIO	3R2J	A4HRG8	123.1 Da LogP 0.78 TPSA 50.2	✓ Ro5	✓ Clean	`c1cc(cnc1)C(=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
ZINC1592410	0.739	212.2 Da LogP 1.54 TPSA 59.9	✓ Ro5	Alert	`O=C(C(=O)c1cccnc1)c1cccnc1`
ZINC100077468	0.643	225.2 Da LogP 2.54 TPSA 47.0	✓ Ro5	✓ Clean	`O=C(CC(=O)c1cccnc1)c1ccccc1`
ZINC8419477	0.633	200.2 Da LogP 1.84 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(O)c1cncc(-c2cccnc2)c1`
ZINC100083979	0.630	226.2 Da LogP 1.93 TPSA 59.9	✓ Ro5	✓ Clean	`O=C(CC(=O)c1cccnc1)c1cccnc1`
ZINC517333	0.625	242.2 Da LogP 2.03 TPSA 79.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2cccnc2)cc1`
ZINC3150114	0.621	296.3 Da LogP 1.07 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(c1cccnc1)N1CCN(C(=O)c2cccnc2)CC1`
ZINC1675504	0.613	289.3 Da LogP 3.20 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(c1cccnc1)C(O)(c1ccccc1)c1ccccc1`
ZINC20442012	0.613	200.2 Da LogP 1.84 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2cccnc2)nc1`
ZINC227663	0.613	295.3 Da LogP 1.68 TPSA 53.5	✓ Ro5	✓ Clean	`O=C(c1ccccc1)N1CCN(C(=O)c2cccnc2)CC1`
ZINC19091377	0.600	201.2 Da LogP 1.24 TPSA 76.0	✓ Ro5	✓ Clean	`O=C(O)c1cnc(-c2cccnc2)nc1`
ZINC1666238	0.594	226.2 Da LogP -1.47 TPSA 102.7	✓ Ro5	✓ Clean	`O=C(NC(CO)(CO)CO)c1cccnc1`
ZINC47214419	0.594	200.2 Da LogP 1.84 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2cccnc2)c1`
ZINC68983603	0.594	215.2 Da LogP 2.57 TPSA 59.4	✓ Ro5	✓ Clean	`O=C(O)c1cccc(Oc2cccnc2)c1`
ZINC7739376	0.588	253.3 Da LogP 2.68 TPSA 67.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/C(=O)c2cccnc2)cc1`
ZINC873432	0.588	242.2 Da LogP 2.03 TPSA 79.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc(NC(=O)c2cccnc2)c1`
ZINC101814612	0.581	225.2 Da LogP 2.86 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(/C=C(\O)c1cccnc1)c1ccccc1`
ZINC3153101	0.581	274.3 Da LogP 4.06 TPSA 33.2	✓ Ro5	✓ Clean	`O=C(c1cccnc1)N(c1ccccc1)c1ccccc1`
ZINC34403957	0.581	259.3 Da LogP 3.98 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1ccc(-c2ccccc2)cc1)c1cccnc1`
ZINC36904276	0.581	215.2 Da LogP 2.57 TPSA 59.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2cccnc2)cc1`
ZINC100198376	0.576	217.1 Da LogP 2.27 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(/C=C(/O)C(F)(F)F)c1cccnc1`
ZINC100925214	0.576	217.1 Da LogP 2.27 TPSA 50.2	✓ Ro5	✓ Clean	`O=C(/C=C(\O)C(F)(F)F)c1cccnc1`
ZINC40909373	0.576	208.2 Da LogP 0.67 TPSA 79.3	✓ Ro5	✓ Clean	`CC(C)(NC(=O)c1cccnc1)C(=O)O`
ZINC82714536	0.576	214.2 Da LogP 2.52 TPSA 62.2	✓ Ro5	✓ Clean	`O=C(O)c1cccc(Nc2cccnc2)c1`
ZINC1511141	0.571	256.3 Da LogP 1.71 TPSA 79.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(CNC(=O)c2cccnc2)cc1`
ZINC1582115	0.567	270.3 Da LogP 0.64 TPSA 84.0	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)c1cccnc1)c1cccnc1`
ZINC1698713	0.567	272.3 Da LogP 1.49 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(OCCOC(=O)c1cccnc1)c1cccnc1`
ZINC241589	0.567	200.2 Da LogP 1.70 TPSA 52.1	✓ Ro5	✓ Clean	`O=C(Oc1cccnc1)c1cccnc1`
ZINC3077252	0.567	318.3 Da LogP 2.98 TPSA 84.0	✓ Ro5	✓ Clean	`O=C(Nc1ccc(NC(=O)c2cccnc2)cc1)c1cccnc1`
ZINC10003088	0.563	269.3 Da LogP 1.24 TPSA 71.1	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)c1cccnc1)c1ccccc1`
ZINC1460938	0.563	204.3 Da LogP 2.10 TPSA 33.2	✓ Ro5	✓ Clean	`O=C(c1cccnc1)N1CCCCCC1`
ZINC15659835	0.563	296.3 Da LogP 1.07 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(c1ccncc1)N1CCN(C(=O)c2cccnc2)CC1`
ZINC1728	0.563	226.3 Da LogP 2.64 TPSA 42.9	✓ Ro5	✓ Clean	`CC(C)(C(=O)c1cccnc1)c1cccnc1`
ZINC22121733	0.563	239.3 Da LogP 3.61 TPSA 30.0	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc(C(=O)c2cccnc2)cc1`
ZINC411478	0.563	317.3 Da LogP 3.59 TPSA 71.1	✓ Ro5	✓ Clean	`O=C(Nc1ccccc1NC(=O)c1cccnc1)c1ccccc1`
ZINC50912929	0.563	214.2 Da LogP 2.52 TPSA 62.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Nc2cccnc2)cc1`
ZINC5864339	0.563	218.3 Da LogP 2.49 TPSA 33.2	✓ Ro5	✓ Clean	`O=C(c1cccnc1)N1CCCCCCC1`
ZINC70915012	0.563	203.2 Da LogP 2.61 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(CCC(F)(F)F)c1cccnc1`
ZINC848974	0.563	317.3 Da LogP 3.59 TPSA 71.1	✓ Ro5	✓ Clean	`O=C(Nc1ccc(NC(=O)c2cccnc2)cc1)c1ccccc1`
ZINC34962972	0.559	216.2 Da LogP 1.97 TPSA 72.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2cccnc2)nc1`
ZINC41538388	0.559	238.3 Da LogP 2.50 TPSA 42.0	✓ Ro5	✓ Clean	`O=C(NC1(c2ccccc2)CC1)c1cccnc1`
ZINC1722453	0.548	225.2 Da LogP 2.52 TPSA 47.0	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C(=O)c2cccnc2)cc1`
ZINC235763	0.548	201.2 Da LogP 2.45 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1ccc(F)cc1)c1cccnc1`
ZINC2584594	0.548	262.1 Da LogP 3.08 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1ccc(Br)cc1)c1cccnc1`
ZINC2748110	0.548	318.3 Da LogP 2.98 TPSA 84.0	✓ Ro5	✓ Clean	`O=C(Nc1ccccc1NC(=O)c1cccnc1)c1cccnc1`
ZINC394834	0.548	217.7 Da LogP 2.97 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1ccc(Cl)cc1)c1cccnc1`
ZINC45028795	0.548	252.1 Da LogP 3.62 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1cccnc1)c1c(Cl)cccc1Cl`
ZINC45028802	0.548	211.3 Da LogP 2.93 TPSA 30.0	✓ Ro5	✓ Clean	`Cc1cccc(C)c1C(=O)c1cccnc1`
ZINC45028779	0.545	251.2 Da LogP 3.33 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(c1ccc(C(F)(F)F)cc1)c1cccnc1`
ZINC4823559	0.545	229.3 Da LogP 3.16 TPSA 30.0	✓ Ro5	✓ Clean	`O=C(SCc1ccccc1)c1cccnc1`
ZINC98214121	0.545	217.2 Da LogP 1.36 TPSA 85.2	✓ Ro5	✓ Clean	`O=C(O)c1cnc(Oc2cccnc2)nc1`

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.