Protein profile

KP13_02409

cytotoxic necrotizing factor-like protein

Genome: KpKP13

Gene: AHE43154.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H1M7

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Amino acids 243

Annotations 4

Features 14

PDB binders 1

Druggability 0.466

Overview

Basic information about this protein and its source genome.

Accession: KP13_02409
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43154.1
Status: annotated
Amino acids: 243
Structure source: AlphaFold + ColabFold

GO:0005507 Binding to a copper (Cu) ion. GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0017061 Catalysis of the reaction: 5'-methylthioadenosine + phosphate = adenine + 5-methylthio-D-ribose 1-phosphate.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 37.5
Human E-value: 2.99e-09
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 53.498
DEG E-value: 8.32e-92
Localization: Unknown
ColabFold pLDDT: 98.1

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 0.466

Structure A0A0H3H1M7

Pocket Pocket 1

P2Rank 0.73

Structure A0A0H3H1M7

Pocket Pocket 1

ColabFold model

FPocket 0.159 · Pocket 2

P2Rank 0.751 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 161 / 4744 genomes with a hit

Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

GO:0005507 Binding to a copper (Cu) ion.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GO:0017061 Catalysis of the reaction: 5'-methylthioadenosine + phosphate = adenine + 5-methylthio-D-ribose 1-phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
1	243	Gene3D	G3DSA:3.60.140.10	-
1	243	InterPro	IPR038371	Multi-copper polyphenol oxidoreductase superfamily
3	242	SUPERFAMILY	SSF64438	CNF1/YfiH-like putative cysteine hydrolases
3	242	InterPro	IPR011324	Cytotoxic necrotizing factor-like, catalytic
1	243	FunFam	G3DSA:3.60.140.10:FF:000001	Polyphenol oxidase
20	241	Pfam	PF02578	Multi-copper polyphenol oxidoreductase laccase
20	241	InterPro	IPR003730	Multi-copper polyphenol oxidoreductase
3	242	PANTHER	PTHR30616	UNCHARACTERIZED PROTEIN YFIH
3	242	InterPro	IPR003730	Multi-copper polyphenol oxidoreductase
26	242	NCBIfam	TIGR00726	peptidoglycan editing factor PgeF
26	242	InterPro	IPR003730	Multi-copper polyphenol oxidoreductase
1	18	ProSiteProfiles	PS51257	Prokaryotic membrane lipoprotein lipid attachment site profile.
64	241	CDD	cd16833	YfiH
64	241	InterPro	IPR003730	Multi-copper polyphenol oxidoreductase

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_A0A0H3H1M7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02409	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				0.466

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	10.12	0.544
2	4.89	0.22
3	1.43	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				11.31	0.605

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.

51 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
NOS	6T1B	P84138	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=…`

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
ZINC16951611	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H…`
ZINC2573068	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@…`
ZINC4015531	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C…`
ZINC5127789	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H…`
ZINC8613160	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@…`
ZINC8613161	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H…`
ZINC8614390	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C…`
ZINC8652273	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@…`
ZINC8652274	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@…`
ZINC8855117	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@…`
ZINC895160	1.000	268.2 Da LogP -2.27 TPSA 133.5	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@…`
ZINC106381023	0.826	267.2 Da LogP -2.30 TPSA 139.3	✓ Ro5	✓ Clean	`N[C@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(=O)[nH]…`
ZINC31542954	0.826	267.2 Da LogP -2.30 TPSA 139.3	✓ Ro5	✓ Clean	`N[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(=O)[nH…`
ZINC31543351	0.826	270.2 Da LogP -1.29 TPSA 113.3	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@…`
ZINC3645702	0.826	267.2 Da LogP -2.30 TPSA 139.3	✓ Ro5	✓ Clean	`N[C@@H]1[C@@H](n2cnc3c(=O)[nH]cnc32)O[C@@H](CO)…`
ZINC4634665	0.826	270.2 Da LogP -1.29 TPSA 113.3	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@…`
ZINC5106288	0.818	270.2 Da LogP -1.29 TPSA 113.3	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CF)[C@@H](O)[C@…`
ZINC5106290	0.818	270.2 Da LogP -1.29 TPSA 113.3	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CF)[C@@H](O)[C…`
ZINC5106293	0.818	270.2 Da LogP -1.29 TPSA 113.3	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CF)[C@@H](O)[C@…`
ZINC5106295	0.818	270.2 Da LogP -1.29 TPSA 113.3	✓ Ro5	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CF)[C@@H](O)[C…`
ZINC4963541	0.787	281.3 Da LogP -2.04 TPSA 125.3	✓ Ro5	✓ Clean	`CN[C@@H]1[C@H](CO)O[C@H](n2cnc3c(=O)[nH]cnc32)[…`
ZINC4963542	0.787	281.3 Da LogP -2.04 TPSA 125.3	✓ Ro5	✓ Clean	`CN[C@H]1[C@H](CO)O[C@H](n2cnc3c(=O)[nH]cnc32)[C…`
ZINC4963543	0.787	281.3 Da LogP -2.04 TPSA 125.3	✓ Ro5	✓ Clean	`CN[C@@H]1[C@@H](CO)O[C@H](n2cnc3c(=O)[nH]cnc32)…`
ZINC4963544	0.787	281.3 Da LogP -2.04 TPSA 125.3	✓ Ro5	✓ Clean	`CN[C@H]1[C@@H](CO)O[C@H](n2cnc3c(=O)[nH]cnc32)[…`
ZINC110928985	0.776	282.3 Da LogP -1.61 TPSA 122.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@@H](O)[C@@H](CO)O[C@H]1n1cnc2c(=O)[n…`
ZINC110928990	0.776	282.3 Da LogP -1.61 TPSA 122.5	✓ Ro5	✓ Clean	`CO[C@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(=O)[nH…`
ZINC34149906	0.776	282.3 Da LogP -1.61 TPSA 122.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](O)[C@@H](CO)O[C@H]1n1cnc2c(=O)[n…`
ZINC44169890	0.755	282.3 Da LogP -1.61 TPSA 122.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@@H](CO)O[C@@H](n2cnc3c(=O)[nH]cnc32…`
ZINC83290873	0.755	282.3 Da LogP -1.61 TPSA 122.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](CO)O[C@H](n2cnc3c(=O)[nH]cnc32)[…`
ZINC83290875	0.755	282.3 Da LogP -1.61 TPSA 122.5	✓ Ro5	✓ Clean	`CO[C@@H]1[C@H](CO)O[C@H](n2cnc3c(=O)[nH]cnc32)[…`
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)[…`
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…`

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.