Protein profile

KP13_00974

o-succinylbenzoate synthase

Genome: KpKP13

Gene: AHE43496.1 menC Structure source: AlphaFold + ColabFold UniProt A0A0H3H0Z7

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Amino acids 321

Annotations 5

Features 20

PDB binders 3

Druggability 0.619

Overview

Basic information about this protein and its source genome.

Accession: KP13_00974
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43496.1 menC
Status: annotated
Amino acids: 321
Structure source: AlphaFold + ColabFold

4.2.1.113

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:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water. GO:0000287 Binding to a magnesium (Mg) ion. GO:0043748 Catalysis of the reaction: 2-succinylbenzoate + H2O = 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate.

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: Unknown
ColabFold pLDDT: 96.05

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 0.619

Structure A0A0H3H0Z7

Pocket Pocket 4

P2Rank 0.632

Structure A0A0H3H0Z7

Pocket Pocket 1

ColabFold model

FPocket 0.733 · Pocket 2

P2Rank 0.599 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 125 / 4744 genomes with a hit

Normalized 0.026

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)

4.2.1.113

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:0016836 Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0043748 Catalysis of the reaction: 2-succinylbenzoate + H2O = 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
1	98	SUPERFAMILY	SSF54826	Enolase N-terminal domain-like
1	98	InterPro	IPR029017	Enolase-like, N-terminal
4	321	Hamap	MF_00470	o-succinylbenzoate synthase [menC].
4	321	InterPro	IPR010196	o-Succinylbenzoate synthase, MenC type1
107	308	SUPERFAMILY	SSF51604	Enolase C-terminal domain-like
107	308	InterPro	IPR036849	Enolase-like, C-terminal domain superfamily
5	314	PANTHER	PTHR48073	O-SUCCINYLBENZOATE SYNTHASE-RELATED
5	311	SFLD	SFLDF00009	o-succinylbenzoate synthase
122	282	Pfam	PF13378	Enolase C-terminal domain-like
122	282	InterPro	IPR029065	Enolase C-terminal domain-like
98	295	Gene3D	G3DSA:3.20.20.120	-
98	295	InterPro	IPR036849	Enolase-like, C-terminal domain superfamily
7	307	NCBIfam	TIGR01927	o-succinylbenzoate synthase
5	311	SFLD	SFLDS00001	Enolase
5	292	CDD	cd03320	OSBS
1	311	Gene3D	G3DSA:3.30.390.10	-
1	311	InterPro	IPR029017	Enolase-like, N-terminal
115	210	SMART	SM00922	MR_MLE_2
115	210	InterPro	IPR013342	Mandelate racemase/muconate lactonizing enzyme, C-terminal
98	295	FunFam	G3DSA:3.20.20.120:FF:000006	o-succinylbenzoate synthase

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_A0A0H3H0Z7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00974	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
4				0.619
2				0.545

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	9.24	0.495
2	1.5	0.022
3	1.47	0.02

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
2				0.733

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	8.92	0.478
2	1.52	0.022
3	1.34	0.015
4	1.14	0.009
5	0.75	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.

53 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
164	1R6W	P29208	240.2 Da LogP -0.02 TPSA 111.9	✓ Ro5	✓ Clean	`C1=C[C@H]([C@@H](C(=C1)C(=O)CCC(=O)O)C(=O)O)O`
OSB	1FHV	P29208	222.2 Da LogP 1.43 TPSA 91.7	✓ Ro5	✓ Clean	`c1ccc(c(c1)C(=O)CCC(=O)O)C(=O)O`
SIN	3GC2	P58486	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)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
ZINC1604722	0.870	326.3 Da LogP 2.93 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)CCC(=O)c1ccccc1C(=O)O`
ZINC2518017	0.679	212.6 Da LogP 2.39 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1ccccc1Cl`
ZINC343704	0.667	208.2 Da LogP 1.04 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CC(=O)c1ccccc1C(=O)O`
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`
ZINC14619964	0.633	206.2 Da LogP 2.76 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)c1ccccc1C(=O)O`
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`
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`
ZINC1594157	0.586	240.3 Da LogP 2.81 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)Cc1ccccc1`
ZINC518924	0.586	284.3 Da LogP 2.51 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1CC(=O)c1ccccc1C(=O)O`
ZINC1572706	0.563	260.2 Da LogP -1.05 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)NCCNC(=O)CCC(=O)O`
ZINC77311440	0.563	238.2 Da LogP 1.02 TPSA 100.9	✓ Ro5	✓ Clean	`O=C(O)CCOC(=O)c1ccccc1C(=O)O`
ZINC2579968	0.559	222.2 Da LogP 2.13 TPSA 63.6	✓ Ro5	✓ Clean	`CCOc1ccccc1C(=O)CCC(=O)O`
ZINC82289160	0.559	221.2 Da LogP 1.30 TPSA 83.5	✓ Ro5	✓ Clean	`O=CNc1ccccc1C(=O)CCC(=O)O`
ZINC1671412	0.533	234.3 Da LogP 2.08 TPSA 71.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)CCC(=O)c1ccccc1`
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`
ZINC9095223	0.533	356.3 Da LogP 1.24 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)NCCNC(=O)c1ccccc1C(=O)O`
ZINC13356583	0.531	207.2 Da LogP 1.71 TPSA 80.4	✓ Ro5	✓ Clean	`Nc1ccccc1C(=O)CCCC(=O)O`
ZINC2378634	0.531	206.2 Da LogP 2.43 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccccc1C(=O)CCCC(=O)O`
ZINC2378735	0.531	210.2 Da LogP 2.26 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)c1ccccc1F`
ZINC2518019	0.531	240.7 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)c1ccccc1Cl`
ZINC2567373	0.531	271.1 Da LogP 2.89 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)c1ccccc1Br`
ZINC2579879	0.531	318.1 Da LogP 2.73 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)c1ccccc1I`
ZINC26895996	0.531	208.2 Da LogP 1.79 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCc1ccccc1C(=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`
ZINC2024475	0.529	251.2 Da LogP 0.98 TPSA 103.7	✓ Ro5	✓ Clean	`O=C(O)CCCNC(=O)c1ccccc1C(=O)O`
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`
ZINC15080701	0.517	222.2 Da LogP 1.43 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1ccc(C(=O)O)cc1`
ZINC1427	0.516	254.3 Da LogP 3.40 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)c1ccc(-c2ccccc2)cc1`
ZINC167997	0.515	209.2 Da LogP 1.27 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)CCNc1ccccc1C(=O)O`
ZINC1721300	0.515	270.3 Da LogP 3.07 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCc1ccccc1-c1ccccc1C(=O)O`
ZINC2378635	0.515	220.3 Da LogP 2.82 TPSA 54.4	✓ Ro5	✓ Clean	`Cc1ccccc1C(=O)CCCCC(=O)O`
ZINC2378696	0.515	242.3 Da LogP 3.28 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)c1cccc2ccccc12`
ZINC2378736	0.515	224.2 Da LogP 2.65 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)c1ccccc1F`
ZINC2518020	0.515	254.7 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)c1ccccc1Cl`
ZINC2518021	0.515	268.7 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)c1ccccc1Cl`
ZINC2567374	0.515	285.1 Da LogP 3.28 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)c1ccccc1Br`
ZINC2579880	0.515	332.1 Da LogP 3.12 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)c1ccccc1I`
ZINC95634282	0.515	220.3 Da LogP 2.69 TPSA 54.4	✓ Ro5	✓ Clean	`CCc1ccccc1C(=O)CCCC(=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.