Protein profile

VK055_1906

3-phytase

Genome: KpATCC43816

Gene: AIK80512.1 phyK Structure source: Experimental + ColabFold UniProt Q84CN9

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Amino acids 421

Annotations 5

Features 18

PDB binders 6

Druggability 0.725

Overview

Basic information about this protein and its source genome.

Accession: VK055_1906
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK80512.1 phyK
Status: annotated
Amino acids: 421
Structure source: Experimental + ColabFold

3.1.3.8

GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall. GO:0016158 Catalysis of the reaction: myo-inositol hexakisphosphate + H2O = D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate. GO:0046872 Binding to a metal ion. GO:0050308 Catalysis of the reaction: sugar phosphate + H2O = sugar + phosphate.

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: Periplasmic
ColabFold pLDDT: 94.52

Selected Druggability evidence

PDB experimental structure

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 0.725

Structure 2WNH

Pocket Pocket 11

P2Rank 0.784

Structure 2WNH

Pocket Pocket 1

ColabFold model

FPocket 0.378 · Pocket 6

P2Rank 0.726 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 15 / 4744 genomes with a hit

Normalized 0.003

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

3.1.3.8

Gene Ontology (GO)

GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
GO:0016158 Catalysis of the reaction: myo-inositol hexakisphosphate + H2O = D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate.
GO:0046872 Binding to a metal ion.
GO:0050308 Catalysis of the reaction: sugar phosphate + H2O = sugar + phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
1	10	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	27	Phobius	SIGNAL_PEPTIDE	Signal peptide region
28	421	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
23	27	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
28	408	SUPERFAMILY	SSF53254	Phosphoglycerate mutase-like
28	408	InterPro	IPR029033	Histidine phosphatase superfamily
11	22	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
32	46	ProSitePatterns	PS00616	Histidine acid phosphatases phosphohistidine signature.
32	46	InterPro	IPR033379	Histidine acid phosphatase active site
1	27	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
31	356	Pfam	PF00328	Histidine phosphatase superfamily (branch 2)
31	356	InterPro	IPR000560	Histidine phosphatase superfamily, clade-2
1	27	SignalP_EUK	SignalP-noTM	SignalP-noTM
26	359	PANTHER	PTHR11567	ACID PHOSPHATASE-RELATED
31	357	CDD	cd07061	HP_HAP_like
31	357	InterPro	IPR000560	Histidine phosphatase superfamily, clade-2
20	421	Gene3D	G3DSA:3.40.50.1240	-
20	421	InterPro	IPR029033	Histidine phosphatase superfamily

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

3 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 2WNH	X-ray	1.68 Å	A,B	93.3% 29-421	PDBe RCSB PDBj File	Viewing
PDB 2WNI	X-ray	2.57 Å	A,B,C,D	93.3% 29-421	PDBe RCSB PDBj File	Loaded
PDB 2WU0	X-ray	2.57 Å	A,B,C,D	93.3% 29-421	PDBe RCSB PDBj File	Loaded
ColabFold VK055_1906	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
23				0.451
49				0.366
1				0.241

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	16.66	0.784
2	16.34	0.777
3	13.24	0.678
4	11.26	0.603
5	11.24	0.602

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
6				0.378

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	8.52	0.455
2	5.28	0.247
3	2.36	0.062
4	1.52	0.022
5	0.73	0.002

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.

56 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
IHP	1DKP	P07102	660.0 Da LogP -3.13 TPSA 400.6	3 viol.	✓ Clean	`C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O…`
IHS	4ARO	H9TUK5	660.5 Da LogP -4.87 TPSA 381.6	3 viol.	✓ Clean	`C1(C(C(C(C(C1OS(=O)(=O)O)OS(=O)(=O)O)OS(=O)(=O)…`
P15	4ARV	H9TUK6	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
TLA	4ARU	H9TUK5	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@@H]([C@H](C(=O)O)O)(C(=O)O)O`
TOE	4ARV	H9TUK6	164.2 Da LogP -0.34 TPSA 47.9	✓ Ro5	✓ Clean	`COCCOCCOCCO`
WO4	1DKO	P07102	247.8 Da LogP -2.62 TPSA 80.3	✓ Ro5	✓ Clean	`[O-][W](=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
ZINC1580161	1.000	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	1.000	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	1.000	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	1.000	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	1.000	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	1.000	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	1.000	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC575419714	0.727	312.4 Da LogP 0.42 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCSCCOCCOCCO`
ZINC13556870	0.722	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@@H](O)[C@@H](O)[C@H](O)[C@@H…`
ZINC71789368	0.722	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](OP(=O)(O)O)[C@@H](O)[C@H]…`
ZINC71792243	0.722	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](O)[C@@H](O)[C@@H…`
ZINC100015956	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](OP(=O)(O)O)[C@H]…`
ZINC100015959	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](OP(=O)(O)O)[C@H]…`
ZINC100016166	0.706	340.1 Da LogP -3.60 TPSA 214.4	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1[C@@H](O)[C@@H](O)[C@@H](OP(=O…`
ZINC100590871	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@H](OP(=O)(O)O)[C@H](…`
ZINC1501016356	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)OC1C(O)[C@H](OP(=O)(O)O)C(O)[C@H](OP(=…`
ZINC115163232	0.700	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCCO`
ZINC258837490	0.700	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCCO`
ZINC12359024	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC13533920	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532740	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC2013424	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC3860635	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O`
ZINC5783661	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC6072527	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1692489	0.688	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC3874716	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC4530388	0.688	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5178829	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5701172	0.688	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC5997861	0.688	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC100016164	0.667	260.1 Da LogP -3.72 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1[C@@H](O)[C@@H](O)[C@@H](O)[C@…`
ZINC100028278	0.667	260.1 Da LogP -3.72 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@@H](O)[C@@H](O)[C@H](O)[C@@H…`
ZINC100061358	0.667	260.1 Da LogP -3.72 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H]…`
ZINC100085584	0.667	260.1 Da LogP -3.72 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@@H](O)[C@H](O)[C@@H](O)[C@H]…`
ZINC100604895	0.667	260.1 Da LogP -3.72 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1[C@@H](O)[C@H](O)[C@H](O)[C@@H…`
ZINC100620447	0.667	260.1 Da LogP -3.72 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H…`
ZINC13536447	0.667	340.1 Da LogP -3.60 TPSA 214.4	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](O)[C@H](O)[C@@H]…`
ZINC2504621	0.667	260.1 Da LogP -3.72 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC1[C@@H](O)[C@H](O)C(O)[C@@H](O)[C@H]…`
ZINC255979099	0.667	260.1 Da LogP -3.72 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1[C@@H](O)[C@@H](O)[C@H](O)[C@@…`
ZINC3869171	0.667	260.1 Da LogP -3.72 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC1[C@H](O)[C@@H](O)C(O)[C@@H](O)[C@H]…`
ZINC3869172	0.667	260.1 Da LogP -3.72 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC1[C@H](O)[C@H](O)C(O)[C@@H](O)[C@H]1O`
ZINC4096301	0.667	340.1 Da LogP -3.60 TPSA 214.4	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1[C@@H](O)[C@@H](O)[C@@H](O)[C@…`
ZINC575432150	0.667	344.4 Da LogP -0.89 TPSA 100.5	✓ Ro5	✓ Clean	`COCCOCCOCCS(=O)(=O)CCOCCOCCO`

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.