Protein profile

KP13_00975

Naphthoate synthase

Genome: KpKP13

Gene: AHE43495.1 menB Structure source: AlphaFold + ColabFold UniProt A0A0H3GR41

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Amino acids 285

Annotations 5

Features 17

PDB binders 12

Druggability 0.936

Overview

Basic information about this protein and its source genome.

Accession: KP13_00975
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43495.1 menB
Status: annotated
Amino acids: 285
Structure source: AlphaFold + ColabFold

4.1.3.36

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: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:0008935 Catalysis of the reaction: 2-succinylbenzoyl-CoA + H+ = 1,4-dihydroxy-2-naphthoyl-CoA + H2O. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 34.783
Human E-value: 2.5e-17
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 89.928
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 98.16

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 0.936

Structure A0A0H3GR41

Pocket Pocket 1

P2Rank 0.783

Structure A0A0H3GR41

Pocket Pocket 1

ColabFold model

FPocket 0.601 · Pocket 1

P2Rank 0.825 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 784 / 4744 genomes with a hit

Normalized 0.165

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)

4.1.3.36

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: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:0008935 Catalysis of the reaction: 2-succinylbenzoyl-CoA + H+ = 1,4-dihydroxy-2-naphthoyl-CoA + H2O.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
223	273	Gene3D	G3DSA:1.10.12.10	-
223	273	InterPro	IPR014748	Enoyl-CoA hydratase, C-terminal
123	143	ProSitePatterns	PS00166	Enoyl-CoA hydratase/isomerase signature.
123	143	InterPro	IPR018376	Enoyl-CoA hydratase/isomerase, conserved site
10	285	PANTHER	PTHR43113	NUCLEOSIDE-DIPHOSPHATE-SUGAR EPIMERASE
22	281	NCBIfam	TIGR01929	1,4-dihydroxy-2-naphthoyl-CoA synthase
22	281	InterPro	IPR010198	1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB
25	221	CDD	cd06558	crotonase-like
15	284	Hamap	MF_01934	1,4-dihydroxy-2-naphthoyl-CoA synthase [menB].
15	284	InterPro	IPR010198	1,4-Dihydroxy-2-naphthoyl-CoA synthase, MenB
223	259	FunFam	G3DSA:1.10.12.10:FF:000002	1,4-dihydroxy-2-naphthoyl-CoA synthase
7	222	FunFam	G3DSA:3.90.226.10:FF:000003	1,4-dihydroxy-2-naphthoyl-CoA synthase
31	279	Pfam	PF00378	Enoyl-CoA hydratase/isomerase
31	279	InterPro	IPR001753	Enoyl-CoA hydratase/isomerase
16	280	SUPERFAMILY	SSF52096	ClpP/crotonase
16	280	InterPro	IPR029045	ClpP/crotonase-like domain superfamily
1	222	Gene3D	G3DSA:3.90.226.10	-

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_A0A0H3GR41	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00975	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				0.936
14				0.244

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				12.61	0.656

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				0.601
9				0.235

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	14.21	0.715
2	1.52	0.022
3	0.86	0.003

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.

72 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
1HA	4I42	P0ABU0	937.7 Da LogP 0.84 TPSA 383.9	3 viol.	✓ Clean	`CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([…`
2NE	4I4Z	P73495	887.6 Da LogP -0.32 TPSA 383.9	3 viol.	✓ Clean	`CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([…`
BTB	4I42	P0ABU0	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
CAA	1Q51	P9WNP5	851.6 Da LogP -1.36 TPSA 380.7	3 viol.	✓ Clean	`CC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P…`
CO8	2DUB	P14604	893.7 Da LogP 1.03 TPSA 363.6	3 viol.	✓ Clean	`CCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P…`
COO	2HW5	P30084	835.6 Da LogP -0.76 TPSA 363.6	3 viol.	✓ Clean	`CC=CC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(C)CO[P@@](…`
DAK	1EY3	P14604	940.8 Da LogP 0.44 TPSA 366.9	3 viol.	Alert	`CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([…`
EP1	1RJN	P9WNP5	252.3 Da LogP -1.13 TPSA 81.1	✓ Ro5	✓ Clean	`C1CN(CCN1CCCS(=O)(=O)O)CCO`
HXC	1MJ3	P14604	865.7 Da LogP 0.25 TPSA 363.6	3 viol.	✓ Clean	`CCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@@…`
MLI	3T89	P0ABU0	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
S0N	3T88	P0ABU0	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](…`
SIN	4ELW	P0ABU0	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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL2024344	P9WNP5	7.31	1012.6 Da LogP 1.17 TPSA 400.9	3 viol.	✓ Clean	`CC(C)(COP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](n2cnc3…`
CHEMBL2024338	P9WNP5	7.01	978.2 Da LogP 0.52 TPSA 400.9	3 viol.	✓ Clean	`CC(C)(COP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](n2cnc3…`
CHEMBL2024339	P9WNP5	6.87	1022.6 Da LogP 0.63 TPSA 400.9	3 viol.	✓ Clean	`CC(C)(COP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](n2cnc3…`
CHEMBL2024341	P9WNP5	6.81	988.7 Da LogP -0.23 TPSA 444.1	3 viol.	✓ Clean	`CC(C)(COP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](n2cnc3…`
DWT	P30084	6.74	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
CHEMBL2024337	P9WNP5	6.69	961.7 Da LogP 0.00 TPSA 400.9	3 viol.	✓ Clean	`CC(C)(COP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](n2cnc3…`
CHEMBL2024335	P9WNP5	6.46	978.2 Da LogP 0.52 TPSA 400.9	3 viol.	✓ Clean	`CC(C)(COP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](n2cnc3…`
CHEMBL2024340	P9WNP5	6.38	1069.6 Da LogP 0.47 TPSA 400.9	3 viol.	✓ Clean	`CC(C)(COP(=O)(O)OP(=O)(O)OC[C@H]1O[C@@H](n2cnc3…`
CHEMBL2024265	P9WNP5	—	345.8 Da LogP 3.96 TPSA 66.4	✓ Ro5	✓ Clean	`CC(C(=O)c1ccc(Cl)cc1)C(N[C@@H](C)c1ccccc1)C(=O)O`
CHEMBL2024334	P9WNP5	—	333.8 Da LogP 3.72 TPSA 66.4	✓ Ro5	✓ Clean	`[2H]C([2H])(C(=O)c1ccccc1Cl)C(N[C@@H](C)c1ccccc…`

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`
ZINC19370281	1.000	252.3 Da LogP -1.13 TPSA 81.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCN1CCN(CCO)CC1`
ZINC34050789	0.885	266.4 Da LogP -0.74 TPSA 81.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCN1CCN(CCO)CC1`
ZINC19798476	0.833	330.4 Da LogP -0.84 TPSA 115.2	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCN1CCN(CCCS(=O)(=O)O)CC1`
ZINC19203136	0.769	238.3 Da LogP -1.52 TPSA 81.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCN1CCN(CCO)CC1`
ZINC19371704	0.731	358.5 Da LogP -0.06 TPSA 115.2	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCN1CCN(CCCCS(=O)(=O)O)CC1`
ZINC1757453	0.679	207.3 Da LogP 0.75 TPSA 57.6	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCN1CCCCC1`
ZINC2004377	0.655	209.3 Da LogP -0.40 TPSA 66.8	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCN1CCOCC1`
ZINC19366017	0.643	224.3 Da LogP -1.56 TPSA 81.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CN1CCN(CCO)CC1`
ZINC38644880	0.633	208.3 Da LogP -0.83 TPSA 69.6	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCN1CCNCC1`
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`
ZINC19364835	0.615	302.4 Da LogP -1.62 TPSA 115.2	✓ Ro5	✓ Clean	`O=S(=O)(O)CCN1CCN(CCS(=O)(=O)O)CC1`
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`
ZINC38748	0.610	259.7 Da LogP 3.83 TPSA 29.1	✓ Ro5	✓ Clean	`C[C@H](NC(=O)c1ccc(Cl)cc1)c1ccccc1`
ZINC38749	0.610	259.7 Da LogP 3.83 TPSA 29.1	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)c1ccc(Cl)cc1)c1ccccc1`
ZINC3206804	0.600	235.3 Da LogP 1.53 TPSA 57.6	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCN1CCCCCC1`
ZINC34616752	0.586	210.3 Da LogP -1.60 TPSA 81.1	✓ Ro5	✓ Clean	`O=S(=O)(O)N1CCN(CCO)CC1`
ZINC2568377	0.581	223.3 Da LogP -0.01 TPSA 66.8	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCN1CCOCC1`
ZINC1557324	0.575	244.7 Da LogP 4.33 TPSA 17.1	✓ Ro5	✓ Clean	`C[C@@H](C(=O)c1ccc(Cl)cc1)c1ccccc1`
ZINC2031878	0.575	244.7 Da LogP 4.33 TPSA 17.1	✓ Ro5	✓ Clean	`C[C@H](C(=O)c1ccc(Cl)cc1)c1ccccc1`
ZINC1572706	0.563	260.2 Da LogP -1.05 TPSA 132.8	✓ Ro5	✓ Clean	`O=C(O)CCC(=O)NCCNC(=O)CCC(=O)O`
ZINC90741911	0.563	222.3 Da LogP -0.44 TPSA 69.6	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCN1CCNCC1`
ZINC21996859	0.561	274.7 Da LogP 3.89 TPSA 37.3	✓ Ro5	✓ Clean	`C[C@H](C(=O)c1ccccc1)[C@@H](O)c1ccc(Cl)cc1`
ZINC21996863	0.561	274.7 Da LogP 3.89 TPSA 37.3	✓ Ro5	✓ Clean	`C[C@@H](C(=O)c1ccccc1)[C@@H](O)c1ccc(Cl)cc1`
ZINC21996865	0.561	274.7 Da LogP 3.89 TPSA 37.3	✓ Ro5	✓ Clean	`C[C@H](C(=O)c1ccccc1)[C@H](O)c1ccc(Cl)cc1`
ZINC21996869	0.561	274.7 Da LogP 3.89 TPSA 37.3	✓ Ro5	✓ Clean	`C[C@@H](C(=O)c1ccccc1)[C@H](O)c1ccc(Cl)cc1`
ZINC36421945	0.556	297.4 Da LogP 3.06 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@H](N[C@@H](CC(=O)c1ccccc1)C(=O)O)c1ccccc1`
ZINC36421946	0.556	297.4 Da LogP 3.06 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@H](N[C@H](CC(=O)c1ccccc1)C(=O)O)c1ccccc1`
ZINC68606053	0.556	297.4 Da LogP 3.06 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@@H](N[C@@H](CC(=O)c1ccccc1)C(=O)O)c1ccccc1`
ZINC68606064	0.556	297.4 Da LogP 3.06 TPSA 66.4	✓ Ro5	✓ Clean	`C[C@@H](N[C@H](CC(=O)c1ccccc1)C(=O)O)c1ccccc1`
ZINC69952221	0.556	312.4 Da LogP 0.46 TPSA 60.9	✓ Ro5	✓ Clean	`O=S(=O)(CCCN1CCN(CCO)CC1)c1ccccc1`
ZINC19594730	0.552	316.4 Da LogP -1.23 TPSA 115.2	✓ Ro5	✓ Clean	`O=S(=O)(O)CCN1CCCN(CCS(=O)(=O)O)CC1`
ZINC71404929	0.552	330.4 Da LogP -0.84 TPSA 115.2	✓ Ro5	✓ Clean	`O=S(=O)(O)CCN1CCCCN(CCS(=O)(=O)O)CC1`
ZINC71606226	0.550	270.7 Da LogP 1.94 TPSA 91.7	✓ Ro5	✓ Clean	`C[C@H](C(=O)c1ccc(Cl)cc1)C(C(=O)O)C(=O)O`
ZINC71606228	0.550	270.7 Da LogP 1.94 TPSA 91.7	✓ Ro5	✓ Clean	`C[C@@H](C(=O)c1ccc(Cl)cc1)C(C(=O)O)C(=O)O`
ZINC220133900	0.538	398.3 Da LogP 3.77 TPSA 85.1	✓ Ro5	✓ Clean	`Cc1nc2nc(-c3cccnc3)nn2cc1C(=O)Nc1cccc(C(F)(F)F)…`
ZINC295648	0.535	259.7 Da LogP 3.83 TPSA 29.1	✓ Ro5	✓ Clean	`C[C@H](NC(=O)c1ccccc1)c1ccc(Cl)cc1`
ZINC295649	0.535	259.7 Da LogP 3.83 TPSA 29.1	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)c1ccccc1)c1ccc(Cl)cc1`
ZINC14788970	0.533	288.8 Da LogP 3.22 TPSA 55.1	✓ Ro5	✓ Clean	`C[C@@H](N[C@@H](C(N)=O)c1ccccc1)c1ccc(Cl)cc1`
ZINC14788974	0.533	288.8 Da LogP 3.22 TPSA 55.1	✓ Ro5	✓ Clean	`C[C@@H](N[C@H](C(N)=O)c1ccccc1)c1ccc(Cl)cc1`
ZINC14788975	0.533	288.8 Da LogP 3.22 TPSA 55.1	✓ Ro5	✓ Clean	`C[C@H](N[C@H](C(N)=O)c1ccccc1)c1ccc(Cl)cc1`
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`

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.