Protein profile

VK055_0866

phenazine biosynthesis, PhzF family protein

Genome: KpATCC43816

Gene: AIK79489.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GN46

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Amino acids 264

Annotations 4

Features 11

PDB binders 5

Druggability 0.532

Overview

Basic information about this protein and its source genome.

Accession: VK055_0866
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79489.1
Status: annotated
Amino acids: 264
Structure source: AlphaFold + ColabFold

GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones. 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0016853 Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 35.315
Human E-value: 5.67e-43
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 29.225
Localization: Cytoplasmic
ColabFold pLDDT: 97.02

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 0.532

Structure A0A0H3GN46

Pocket Pocket 12

P2Rank 0.816

Structure A0A0H3GN46

Pocket Pocket 1

ColabFold model

FPocket 0.71 · Pocket 8

P2Rank 0.813 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 58 / 4744 genomes with a hit

Normalized 0.012

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0016853 Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records

Show feature table

Start	End	DB	Term	Name
6	254	Gene3D	G3DSA:3.10.310.10	Diaminopimelate Epimerase; Chain A, domain 1
9	258	Pfam	PF02567	Phenazine biosynthesis-like protein
9	258	InterPro	IPR003719	Phenazine biosynthesis PhzF-like
5	261	PANTHER	PTHR13774	PHENAZINE BIOSYNTHESIS PROTEIN
5	261	InterPro	IPR003719	Phenazine biosynthesis PhzF-like
3	262	SUPERFAMILY	SSF54506	Diaminopimelate epimerase-like
119	250	Gene3D	G3DSA:3.10.310.10	Diaminopimelate Epimerase; Chain A, domain 1
3	231	NCBIfam	TIGR00654	PhzF family phenazine biosynthesis isomerase
3	231	InterPro	IPR003719	Phenazine biosynthesis PhzF-like
1	262	PIRSF	PIRSF016184	Ismrse_PhzF
1	262	InterPro	IPR003719	Phenazine biosynthesis PhzF-like

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_A0A0H3GN46	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0866	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
15				0.241
6				0.001
18				0.0

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				21.7	0.816

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
8				0.71
16				0.107
1				0.008
13				0.0

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				21.58	0.813
2				0.92	0.004

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.

55 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
3HA	1U1W	Q51792	153.1 Da LogP 0.67 TPSA 83.5	✓ Ro5	✓ Clean	`c1cc(c(c(c1)O)N)C(=O)O`
BTB	4DUN	Q186X0	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
HHA	1U1X	Q51792	155.2 Da LogP -0.74 TPSA 83.5	✓ Ro5	✓ Clean	`C1=C[C@@H]([C@H](C(=C1)C(=O)O)N)O`
SIN	3EDN	A0A6L8PH16	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)O`
W81	5IWE	Q51792	183.2 Da LogP -1.75 TPSA 77.0	✓ Ro5	✓ Clean	`CCO[C@@H]1C=CC=C([C@H]1[NH3+])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
ZINC1615342	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC1703679	0.630	216.0 Da LogP 1.73 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1c(Br)cccc1C(=O)O`
ZINC1721751	0.630	263.0 Da LogP 1.57 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1c(I)cccc1C(=O)O`
ZINC1529497	0.615	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045	0.615	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115	0.615	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020	0.615	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440	0.615	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298	0.615	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062	0.615	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC1081205	0.567	205.1 Da LogP 1.99 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1c(C(=O)O)cccc1C(F)(F)F`
ZINC1572706	0.563	260.2 Da LogP -1.05 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)NCCNC(=O)CCC(=O)O`
ZINC82369423	0.556	217.0 Da LogP 1.85 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(O)c1Br`
ZINC95713705	0.556	264.0 Da LogP 1.70 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(O)c1I`
ZINC3869266	0.545	224.2 Da LogP -0.04 TPSA 126.6	✓ Ro5	✓ Clean	`Nc1c(O)cccc1C(=O)C[C@H](N)C(=O)O`
ZINC901507	0.545	224.2 Da LogP -0.04 TPSA 126.6	✓ Ro5	✓ Clean	`Nc1c(O)cccc1C(=O)C[C@@H](N)C(=O)O`
ZINC1600331	0.542	330.2 Da LogP 2.15 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)O)c1-c1c(C(=O)O)cccc1C(=O)O`
ZINC1703342	0.533	202.2 Da LogP 1.07 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)CCCC(=O)O`
ZINC1728397	0.533	233.2 Da LogP -0.29 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)CCN(CCC(=O)O)CCC(=O)O`
ZINC2508031	0.533	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)CCCCC(=O)O`
ZINC2517013	0.533	250.2 Da LogP 0.89 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)CCP(CCC(=O)O)CCC(=O)O`
ZINC1697439	0.529	219.5 Da LogP 1.79 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)C(Cl)(Cl)Cl`
ZINC35465466	0.529	244.3 Da LogP 2.24 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCC(=O)CCC(=O)O`
ZINC39208104	0.529	262.2 Da LogP -0.20 TPSA 127.2	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)OCCOC(=O)CCC(=O)O`
ZINC27644343	0.528	364.4 Da LogP 3.25 TPSA 139.0	✓ Ro5	✓ Clean	`Nc1c(O)ccc2c1Oc1c(ccc(O)c1N)C2c1ccccc1C(=O)O`
ZINC2334905	0.522	261.4 Da LogP 1.10 TPSA 63.9	✓ Ro5	✓ Clean	`CC(C)CCN(CCC(C)C)C(CO)(CO)CO`
ZINC3159953	0.522	261.4 Da LogP 1.38 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCN(CCCCC)C(CO)(CO)CO`
ZINC388710	0.520	210.1 Da LogP 0.78 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)O)c1C(=O)O`
ZINC45070868	0.520	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1cccc2c(C(=O)O)cccc12`
ZINC1715583	0.519	225.2 Da LogP 0.36 TPSA 137.9	✓ Ro5	✓ Clean	`Nc1c(C(=O)O)ccc(C(=O)O)c1C(=O)O`
ZINC40564457	0.517	263.0 Da LogP 1.57 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)O)c1I`
ZINC40564460	0.517	216.0 Da LogP 1.73 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)O)c1Br`
ZINC13352595	0.515	221.1 Da LogP 1.87 TPSA 72.5	✓ Ro5	✓ Clean	`Nc1c(OC(F)(F)F)cccc1C(=O)O`
ZINC77270957	0.515	320.1 Da LogP 2.96 TPSA 80.4	✓ Ro5	Alert	`Nc1c(C(=O)O)cccc1C(=O)c1ccc(Br)cc1`
ZINC1542984448	0.500	470.5 Da LogP 0.07 TPSA 148.4	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC1586444	0.500	210.2 Da LogP -0.65 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)CCS(=O)(=O)CCC(=O)O`
ZINC1753095	0.500	238.3 Da LogP 1.40 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCSCCSCCC(=O)O`
ZINC22028383	0.500	204.2 Da LogP -0.88 TPSA 98.7	✓ Ro5	✓ Clean	`O=C(O)CCNCCNCCC(=O)O`
ZINC22576322	0.500	348.4 Da LogP -0.51 TPSA 155.7	✓ Ro5	✓ Clean	`O=C(O)CCN(CCC(=O)O)CCN(CCC(=O)O)CCC(=O)O`
ZINC26897400	0.500	286.4 Da LogP 3.41 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCCC(=O)O`
ZINC35977596	0.500	294.3 Da LogP 0.00 TPSA 111.5	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCC(=O)O`
ZINC38682833	0.500	286.3 Da LogP -0.61 TPSA 115.2	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)N1CCN(C(=O)CCC(=O)O)CC1`
ZINC39383060	0.500	206.2 Da LogP -0.03 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCC(=O)O`
ZINC39427081	0.500	250.2 Da LogP -0.01 TPSA 102.3	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCC(=O)O`
ZINC4181831	0.500	232.2 Da LogP -0.01 TPSA 129.0	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)C(CC(=O)O)CC(=O)O`
ZINC4822898	0.500	272.3 Da LogP 3.02 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCC(=O)O`
ZINC4822900	0.500	300.4 Da LogP 3.80 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCC(=O)O`
ZINC71257127	0.500	426.5 Da LogP 0.05 TPSA 139.2	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCC(=O)O`
ZINC71257128	0.500	338.4 Da LogP 0.02 TPSA 120.8	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCC(=O)O`
ZINC79016464	0.500	382.4 Da LogP 0.04 TPSA 130.0	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCC(=O)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.