Protein profile

KP13_00978

Menaquinone-specific isochorismate synthase

Genome: KpKP13

Gene: menF AHE43492.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GT11

Export view

Amino acids 429

Annotations 5

Features 13

PDB binders 6

Druggability 0.887

Overview

Basic information about this protein and its source genome.

Accession: KP13_00978
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: menF AHE43492.1
Status: annotated
Amino acids: 429
Structure source: AlphaFold + ColabFold

5.4.4.2

GO:0009234 The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2. 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:0008909 Catalysis of the reaction: chorismate = isochorismate. GO:0000287 Binding to a magnesium (Mg) ion.

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: 95.92

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 0.887

Structure A0A0H3GT11

Pocket Pocket 1

P2Rank 0.888

Structure A0A0H3GT11

Pocket Pocket 1

ColabFold model

FPocket 0.37 · Pocket 1

P2Rank 0.897 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 63 / 4744 genomes with a hit

Normalized 0.013

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)

5.4.4.2

Gene Ontology (GO)

GO:0009234 The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
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:0008909 Catalysis of the reaction: chorismate = isochorismate.
GO:0000287 Binding to a magnesium (Mg) ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
3	429	Hamap	MF_01935	Isochorismate synthase MenF [menF].
3	429	InterPro	IPR034681	Isochorismate synthase MenF
92	426	NCBIfam	TIGR00543	isochorismate synthase
92	426	InterPro	IPR004561	Isochorismate synthase
9	427	PANTHER	PTHR47253	-
9	427	InterPro	IPR044250	Isochorismate synthase MenF-like
1	428	Gene3D	G3DSA:3.60.120.10	Anthranilate synthase
1	428	InterPro	IPR005801	ADC synthase
24	427	SUPERFAMILY	SSF56322	ADC synthase
24	427	InterPro	IPR005801	ADC synthase
1	429	FunFam	G3DSA:3.60.120.10:FF:000002	Isochorismate synthase MenF
169	419	Pfam	PF00425	chorismate binding enzyme
169	419	InterPro	IPR015890	Chorismate-utilising enzyme, C-terminal

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...

Legend High Medium Low

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_A0A0H3GT11	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00978	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				0.887
19				0.264

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	16.81	0.788
2	1.73	0.031
3	1.63	0.026
4	1.32	0.015

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				0.37

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	15.68	0.759
2	1.9	0.038
3	1.56	0.024

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.

70 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
15P	3OS6	A0A6H3A7J7	1529.8 Da LogP 0.17 TPSA 334.1	2 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO…`
ISC	5JXZ	P0AEJ3	226.2 Da LogP -0.09 TPSA 104.1	✓ Ro5	✓ Clean	`C=C(C(=O)O)O[C@H]1C=CC=C([C@@H]1O)C(=O)O`
ISJ	5JXZ	P0AEJ3	226.2 Da LogP -0.09 TPSA 104.1	✓ Ro5	✓ Clean	`C=C(C(=O)O)O[C@@H]1C=C(C=C[C@H]1O)C(=O)O`
PYR	2FN1	Q9X9I8	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)C(=O)O`
SAL	2FN1	Q9X9I8	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1ccc(c(c1)C(=O)O)O`
TAR	2EUA	P38051	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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL3343825	Q9X9I8	6.10	316.2 Da LogP 1.82 TPSA 152.0	✓ Ro5	Alert	`COC(=O)Oc1c([N+](=O)[O-])cc2oc(=O)sc2c1[N+](=O)…`
CHEMBL1088356	P0AEJ2	—	506.0 Da LogP 1.70 TPSA 190.7	1 viol.	✓ Clean	`Cc1ccc(C(=O)N[C@@H](CCCCN)C(=O)N[C@@H](Cc2cccc(…`
CHEMBL1088493	P0AEJ2	—	570.6 Da LogP 1.17 TPSA 217.4	2 viol.	✓ Clean	`NC(=O)C1(NC(=O)[C@H](CCCNC(=O)c2cccc(OCC(=O)O)c…`
CHEMBL1094067	P0AEJ2	—	660.6 Da LogP 1.47 TPSA 264.1	2 viol.	✓ Clean	`Cc1ccc(C(=O)N[C@@H](CCCNC(=O)c2cccc(OCC(=O)O)c2…`
CHEMBL1094068	P0AEJ2	—	643.7 Da LogP 2.39 TPSA 206.9	1 viol.	✓ Clean	`NC(=O)C1(NC(=O)[C@H](CCCNC(=O)c2cccc(OCC(=O)O)c…`
CHEMBL1094069	P0AEJ2	—	751.8 Da LogP 4.53 TPSA 233.2	1 viol.	✓ Clean	`CC(C(=O)N[C@@H](CCCNC(=O)c1cccc(OCC(=O)O)c1)C(=…`
CHEMBL1094070	P0AEJ2	—	681.7 Da LogP 1.30 TPSA 258.8	3 viol.	✓ Clean	`COc1cc(OC)cc(C(=O)N[C@@H](CCCNC(=O)c2cccc(OCC(=…`
CHEMBL1094071	P0AEJ2	—	680.7 Da LogP 1.80 TPSA 220.3	1 viol.	✓ Clean	`NC(=O)C1(NC(=O)[C@H](CCCNC(=O)c2cccc(OCC(=O)O)c…`
CHEMBL1094072	P0AEJ2	—	670.1 Da LogP 2.25 TPSA 240.3	2 viol.	✓ Clean	`Cc1ccc(C(=O)N[C@@H](CCCNC(=O)c2cccc(OCC(=O)O)c2…`
CHEMBL1094717	P0AEJ2	—	448.9 Da LogP 1.59 TPSA 164.7	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)N[C@@H](C)C(=O)N[C@@H](Cc2cccc(Cl)c…`
CHEMBL1095961	P0AEJ2	—	716.2 Da LogP 2.59 TPSA 240.3	2 viol.	✓ Clean	`Cc1ccc(C(=O)N[C@@H](CSCCCNC(=O)c2cccc(OCC(=O)O)…`
CHEMBL216545	P0AEJ2	—	196.2 Da LogP 0.85 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)COc1cccc(C(=O)O)c1`
CHEMBL216601	P0AEJ2	—	195.2 Da LogP 0.25 TPSA 89.6	✓ Ro5	✓ Clean	`NC(=O)c1cccc(OCC(=O)O)c1`
CHEMBL385837	P0AEJ2	—	684.1 Da LogP 2.64 TPSA 240.3	2 viol.	✓ Clean	`Cc1ccc(C(=O)N[C@@H](CCCCNC(=O)c2cccc(OCC(=O)O)c…`

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`
ZINC2186720	1.000	316.2 Da LogP 1.82 TPSA 152.0	✓ Ro5	Alert	`COC(=O)Oc1c([N+](=O)[O-])cc2oc(=O)sc2c1[N+](=O)…`
ZINC34317654	1.000	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3869469	1.000	226.2 Da LogP -0.09 TPSA 104.1	✓ Ro5	✓ Clean	`C=C(O[C@@H]1C=C(C(=O)O)C=C[C@@H]1O)C(=O)O`
ZINC3869470	1.000	226.2 Da LogP -0.09 TPSA 104.1	✓ Ro5	✓ Clean	`C=C(O[C@H]1C=C(C(=O)O)C=C[C@@H]1O)C(=O)O`
ZINC3869471	1.000	226.2 Da LogP -0.09 TPSA 104.1	✓ Ro5	✓ Clean	`C=C(O[C@@H]1C=C(C(=O)O)C=C[C@H]1O)C(=O)O`
ZINC3869472	1.000	226.2 Da LogP -0.09 TPSA 104.1	✓ Ro5	✓ Clean	`C=C(O[C@H]1C=C(C(=O)O)C=C[C@H]1O)C(=O)O`
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`
ZINC1445389	0.783	350.1 Da LogP 2.67 TPSA 108.9	✓ Ro5	Alert	`COC(=O)Oc1c(Br)cc2oc(=O)sc2c1[N+](=O)[O-]`
ZINC332363	0.750	226.2 Da LogP 0.61 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)COc1cccc(OCC(=O)O)c1`
ZINC575419714	0.727	312.4 Da LogP 0.42 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCSCCOCCOCCO`
ZINC19432051	0.714	209.2 Da LogP 0.64 TPSA 89.6	✓ Ro5	✓ Clean	`NC(=O)c1cccc(OCCC(=O)O)c1`
ZINC19504011	0.706	210.2 Da LogP 0.94 TPSA 72.8	✓ Ro5	✓ Clean	`COC(=O)COc1cccc(C(=O)O)c1`
ZINC34161407	0.706	210.2 Da LogP 0.94 TPSA 72.8	✓ Ro5	✓ Clean	`COC(=O)c1cccc(OCC(=O)O)c1`
ZINC6743571	0.706	257.3 Da LogP 2.24 TPSA 61.6	✓ Ro5	✓ Clean	`NC(=O)c1cccc(OCCOc2ccccc2)c1`
ZINC115163232	0.700	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCCO`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC258837490	0.700	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCCO`
ZINC20368408	0.694	209.2 Da LogP 0.34 TPSA 78.6	✓ Ro5	✓ Clean	`COC(=O)COc1cccc(C(N)=O)c1`
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`
ZINC36904157	0.688	278.0 Da LogP 1.75 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)COc1cccc(I)c1`
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`
ZINC6743468	0.688	258.3 Da LogP 2.84 TPSA 55.8	✓ Ro5	✓ Clean	`O=C(O)c1cccc(OCCOc2ccccc2)c1`
ZINC19396530	0.686	209.2 Da LogP 0.51 TPSA 75.6	✓ Ro5	✓ Clean	`CNC(=O)COc1cccc(C(=O)O)c1`
ZINC20271516	0.686	209.2 Da LogP 0.51 TPSA 75.6	✓ Ro5	✓ Clean	`CNC(=O)c1cccc(OCC(=O)O)c1`
ZINC21952551	0.686	223.2 Da LogP 0.85 TPSA 66.8	✓ Ro5	✓ Clean	`CN(C)C(=O)COc1cccc(C(=O)O)c1`
ZINC58329168	0.686	271.3 Da LogP 2.63 TPSA 61.6	✓ Ro5	✓ Clean	`NC(=O)c1cccc(OCCCOc2ccccc2)c1`
ZINC70461259	0.684	270.3 Da LogP 1.80 TPSA 81.4	✓ Ro5	✓ Clean	`NC(=O)c1cccc(OCC(=O)Nc2ccccc2)c1`

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.