Protein profile

KP13_00973

2-succinylbenzoate--CoA ligase

Genome: KpKP13

Gene: AHE43497.1 menE Structure source: AlphaFold + ColabFold UniProt A0A0H3GT05

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Amino acids 458

Annotations 3

Features 15

PDB binders 12

Druggability 0.121

Overview

Basic information about this protein and its source genome.

Accession: KP13_00973
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43497.1 menE
Status: annotated
Amino acids: 458
Structure source: AlphaFold + ColabFold

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0008756 Catalysis of the reaction: 2-succinylbenzoate + ATP + CoA = 2-succinylbenzoyl-CoA + AMP + diphosphate. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 30.952
Human E-value: 3.2e-12
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 73.894
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 92.35

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 0.121

Structure A0A0H3GT05

Pocket Pocket 19

P2Rank 0.952

Structure A0A0H3GT05

Pocket Pocket 1

ColabFold model

FPocket 0.087 · Pocket 9

P2Rank 0.964 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 98 / 4744 genomes with a hit

Normalized 0.021

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0008756 Catalysis of the reaction: 2-succinylbenzoate + ATP + CoA = 2-succinylbenzoyl-CoA + AMP + diphosphate.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
139	150	ProSitePatterns	PS00455	Putative AMP-binding domain signature.
139	150	InterPro	IPR020845	AMP-binding, conserved site
8	350	Gene3D	G3DSA:3.40.50.12780	-
8	350	InterPro	IPR042099	ANL, N-terminal domain
13	455	PANTHER	PTHR43767	LONG-CHAIN-FATTY-ACID--COA LIGASE
366	429	Pfam	PF13193	AMP-binding enzyme C-terminal domain
366	429	InterPro	IPR025110	AMP-binding enzyme, C-terminal domain
135	449	CDD	cd17630	OSB_MenE-like
351	454	Gene3D	G3DSA:3.30.300.30	-
351	454	InterPro	IPR045851	AMP-binding enzyme, C-terminal domain superfamily
10	355	Pfam	PF00501	AMP-binding enzyme
10	355	InterPro	IPR000873	AMP-dependent synthetase/ligase domain
29	445	NCBIfam	TIGR01923	o-succinylbenzoate--CoA ligase
29	445	InterPro	IPR010192	2-succinylbenzoate--CoA ligase
8	452	SUPERFAMILY	SSF56801	Acetyl-CoA synthetase-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_A0A0H3GT05	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00973	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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	11.05	0.593
2	5.89	0.288
3	4.3	0.178
4	2.58	0.074
5	2.26	0.056

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	23.6	0.89
2	3.52	0.129
3	2.81	0.087
4	2.03	0.044
5	1.71	0.03

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.

62 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
00A	3CW8	Q8GN86	485.8 Da LogP 0.66 TPSA 192.1	1 viol.	✓ Clean	`c1cc(ccc1C(=O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]…`
01A	3CW9	Q8GN86	920.1 Da LogP 0.67 TPSA 363.6	3 viol.	✓ Clean	`CC(C)(CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]…`
174	1T5D	Q8GN86	156.6 Da LogP 2.04 TPSA 37.3	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)O)Cl`
34Z	2QVY	Q8GN86	191.0 Da LogP 2.69 TPSA 37.3	✓ Ro5	✓ Clean	`c1cc(c(cc1C(=O)O)Cl)Cl`
3BZ	2QVX	Q8GN86	156.6 Da LogP 2.04 TPSA 37.3	✓ Ro5	✓ Clean	`c1cc(cc(c1)Cl)C(=O)O`
4YB	5C5H	P37353	550.5 Da LogP -1.23 TPSA 246.1	2 viol.	✓ Clean	`c1ccc(c(c1)C(=O)CCC(=O)NS(=O)(=O)OC[C@@H]2[C@H]…`
ANP	1V25	Q5SKN9	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
JSA	5ZRN	P9WQ37	530.6 Da LogP 1.12 TPSA 194.9	2 viol.	✓ Clean	`CCCCCCCCCCC[C@H](NS(=O)(=O)OC[C@@H]1[C@H]([C@H]…`
KOY	6NJ0	P37353	519.5 Da LogP 1.62 TPSA 182.9	2 viol.	✓ Clean	`c1ccc(c(c1)C(=O)CCc2cccc(c2)OC[C@@H]3[C@H]([C@H…`
MLI	3R44	P9WQ37	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
OSB	5GTD	P23971	222.2 Da LogP 1.43 TPSA 91.7	✓ Ro5	✓ Clean	`c1ccc(c(c1)C(=O)CCC(=O)O)C(=O)O`
S0N	5X8F	P23971	954.7 Da LogP -1.12 TPSA 430.0	3 viol.	✓ Clean	`CC(C)(CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H](…`

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
ZINC1604722	0.870	326.3 Da LogP 2.93 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)CCC(=O)c1ccccc1C(=O)O`
ZINC1665234	0.850	260.7 Da LogP 3.27 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(Cl)cc2)cc1`
ZINC168462	0.850	232.7 Da LogP 3.71 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(Cl)cc2)cc1`
ZINC2574061	0.769	232.7 Da LogP 3.71 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2cccc(Cl)c2)c1`
ZINC2386680	0.739	248.7 Da LogP 3.83 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(Cl)cc2)cc1`
ZINC2567514	0.739	279.1 Da LogP 4.06 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1cccc(Cl)c1)c1cccc(Cl)c1`
ZINC3200334	0.739	264.7 Da LogP 4.19 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Sc2ccc(Cl)cc2)cc1`
ZINC50913005	0.739	247.7 Da LogP 3.78 TPSA 49.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Nc2ccc(Cl)cc2)cc1`
ZINC1599900	0.720	244.7 Da LogP 3.41 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1cccc(Cl)c1)c1ccccc1`
ZINC14967098	0.714	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC218033334	0.714	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC218033425	0.714	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC218033503	0.714	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC1599892	0.708	251.1 Da LogP 4.22 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(c1cccc(Cl)c1)c1cccc(Cl)c1`
ZINC1601965	0.708	200.6 Da LogP 1.74 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Cl)c(C(=O)O)c1`
ZINC1665257	0.708	274.7 Da LogP 4.36 TPSA 37.3	✓ Ro5	✓ Clean	`CC(C)(c1ccc(Cl)cc1)c1ccc(C(=O)O)cc1`
ZINC105316	0.692	216.7 Da LogP 3.57 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(c1ccccc1)c1cccc(Cl)c1`
ZINC2386679	0.692	267.1 Da LogP 4.36 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(Cl)c(Cl)c2)cc1`
ZINC1555402	0.684	279.1 Da LogP 4.06 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1ccc(Cl)cc1)c1ccc(Cl)cc1`
ZINC1571070	0.680	200.6 Da LogP 1.74 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)O)c(Cl)c1`
ZINC37378035	0.680	219.0 Da LogP 2.26 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)C(=O)c1ccc(Cl)c(Cl)c1`
ZINC4776651	0.680	290.7 Da LogP 3.68 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(Nc1ccc(Cl)cc1)Nc1ccc(C(=O)O)cc1`
ZINC2518017	0.679	212.6 Da LogP 2.39 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1ccccc1Cl`
ZINC1184484	0.677	394.8 Da LogP 4.54 TPSA 95.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(NC(=O)c2cccc(NC(=O)c3cccc(Cl)c3)c2…`
ZINC307519262	0.667	257.9 Da LogP 3.89 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(c1cccc(Cl)c1)C(Cl)(Cl)Cl`
ZINC343704	0.667	208.2 Da LogP 1.04 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CC(=O)c1ccccc1C(=O)O`
ZINC71405457	0.656	278.7 Da LogP 3.41 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(F)c(C(=O)c2cccc(Cl)c2)c1`
ZINC2567379	0.655	257.1 Da LogP 2.50 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1ccccc1Br`
ZINC2579878	0.655	304.1 Da LogP 2.34 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1ccccc1I`
ZINC12359380	0.654	235.5 Da LogP 2.80 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Br)c(Cl)c1`
ZINC196253320	0.654	292.4 Da LogP 4.55 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(c1ccc(Cl)c(Cl)c1)C(Cl)(Cl)Cl`
ZINC2568089	0.654	235.5 Da LogP 2.80 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Cl)c(Br)c1`
ZINC2571851	0.654	282.5 Da LogP 2.64 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Cl)c(I)c1`
ZINC3157259	0.654	275.7 Da LogP 3.29 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2ccc(Cl)cc2)cc1`
ZINC40571399	0.654	282.5 Da LogP 2.64 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)c(Cl)c1`
ZINC4670141	0.654	275.7 Da LogP 3.33 TPSA 49.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(CNCc2ccc(Cl)cc2)cc1`
ZINC5768361	0.654	276.7 Da LogP 3.26 TPSA 63.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(=O)c2ccc(Cl)cc2)cc1`
ZINC388094	0.650	251.1 Da LogP 4.22 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(c1ccc(Cl)cc1)c1ccc(Cl)cc1`
ZINC147806	0.645	290.7 Da LogP 3.68 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(Nc1cccc(Cl)c1)Nc1cccc(C(=O)O)c1`
ZINC2565657	0.643	208.6 Da LogP 3.08 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(c1cccc(Cl)c1)C(F)(F)F`
ZINC2170331	0.636	244.7 Da LogP 3.41 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1ccc(Cl)cc1)c1ccccc1`
ZINC14619964	0.633	206.2 Da LogP 2.76 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)c1ccccc1C(=O)O`
ZINC216777092	0.633	311.1 Da LogP 3.91 TPSA 63.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(=O)c2ccc(Cl)c(Cl)c2)cc1`
ZINC236510	0.633	228.2 Da LogP 2.89 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1cccc2ccccc12`
ZINC52201682	0.633	206.2 Da LogP 2.30 TPSA 54.4	✓ Ro5	✓ Clean	`CCc1ccccc1C(=O)CCC(=O)O`
ZINC114185151	0.632	298.2 Da LogP 2.15 TPSA 108.7	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC28567519	0.632	466.4 Da LogP -1.00 TPSA 215.5	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)/N=C(\O)…`
ZINC15441610	0.630	285.6 Da LogP 4.88 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(c1cccc(Cl)c1)c1cc(Cl)cc(Cl)c1`
ZINC2378575	0.630	243.0 Da LogP 3.74 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(c1ccc(Cl)c(Cl)c1)C(F)(F)F`
ZINC2514256	0.630	231.1 Da LogP 4.22 TPSA 17.1	✓ Ro5	✓ Clean	`CC(C)(C)C(=O)c1ccc(Cl)c(Cl)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.