Protein profile

VK055_0613

benzoate 1,2-dioxygenase electron transfer component

Genome: KpATCC43816

Gene: benC AIK79236.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQC4

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Amino acids 338

Annotations 3

Features 43

PDB binders 7

Druggability 0.852

Overview

Basic information about this protein and its source genome.

Accession: VK055_0613
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: benC AIK79236.1
Status: annotated
Amino acids: 338
Structure source: AlphaFold + ColabFold

GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 24.498
Human E-value: 1.17e-07
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 38.757
Localization: Cytoplasmic
ColabFold pLDDT: 92.34

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 0.852

Structure A0A0H3GQC4

Pocket Pocket 19

P2Rank 0.742

Structure A0A0H3GQC4

Pocket Pocket 1

ColabFold model

FPocket 0.728 · Pocket 11

P2Rank 0.665 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 20 / 4744 genomes with a hit

Normalized 0.004

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Sequence Features

Domain/signature hits from InterPro and related databases.

43 records

Show feature table

Start	End	DB	Term	Name
40	48	ProSitePatterns	PS00197	2Fe-2S ferredoxin-type iron-sulfur binding region signature.
40	48	InterPro	IPR006058	2Fe-2S ferredoxin, iron-sulphur binding site
110	200	Pfam	PF00970	Oxidoreductase FAD-binding domain
110	200	InterPro	IPR008333	Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain
104	202	ProSiteProfiles	PS51384	Ferredoxin reductase-type FAD binding domain profile.
104	202	InterPro	IPR017927	FAD-binding domain, ferredoxin reductase-type
109	331	CDD	cd06209	BenDO_FAD_NAD
109	331	InterPro	IPR047683	Benzoate 1,2-dioxygenase reductase, FAD/NAD binding domain
194	203	PRINTS	PR00410	Phenol hydroxylase reductase family signature
234	243	PRINTS	PR00410	Phenol hydroxylase reductase family signature
298	306	PRINTS	PR00410	Phenol hydroxylase reductase family signature
134	146	PRINTS	PR00410	Phenol hydroxylase reductase family signature
209	228	PRINTS	PR00410	Phenol hydroxylase reductase family signature
151	158	PRINTS	PR00410	Phenol hydroxylase reductase family signature
16	92	PANTHER	PTHR47354	NADH OXIDOREDUCTASE HCR
101	197	Gene3D	G3DSA:2.40.30.10	Translation factors
3	97	ProSiteProfiles	PS51085	2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
3	97	InterPro	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain
210	312	Pfam	PF00175	Oxidoreductase NAD-binding domain
210	312	InterPro	IPR001433	Oxidoreductase FAD/NAD(P)-binding
78	203	SUPERFAMILY	SSF63380	Riboflavin synthase domain-like
78	203	InterPro	IPR017938	Riboflavin synthase-like beta-barrel
200	332	SUPERFAMILY	SSF52343	Ferredoxin reductase-like, C-terminal NADP-linked domain
200	332	InterPro	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
5	94	SUPERFAMILY	SSF54292	2Fe-2S ferredoxin-like
5	94	InterPro	IPR036010	2Fe-2S ferredoxin-like superfamily
3	333	NCBIfam	NF040810	benzoate 1,2-dioxygenase electron transfer component BenC
17	92	CDD	cd00207	fer2
17	92	InterPro	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain
198	330	Gene3D	G3DSA:3.40.50.80	-
198	330	InterPro	IPR039261	Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
1	100	Gene3D	G3DSA:3.10.20.30	-
1	100	InterPro	IPR012675	Beta-grasp domain superfamily
209	228	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
209	228	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
298	306	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
298	306	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
151	158	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
151	158	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
134	144	PRINTS	PR00371	Flavoprotein pyridine nucleotide cytochrome reductase signature
134	144	InterPro	IPR001709	Flavoprotein pyridine nucleotide cytochrome reductase
10	86	Pfam	PF00111	2Fe-2S iron-sulfur cluster binding domain
10	86	InterPro	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain

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_A0A0H3GQC4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0613	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
19				0.852

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	10.16	0.546
2	6.88	0.354
3	5.78	0.281
4	4.11	0.166
5	3.38	0.12

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
11				0.728
15				0.351

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	9.58	0.515
2	9.54	0.513
3	5.21	0.242
4	3.11	0.104
5	2.94	0.094

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.

57 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
BTB	4WQM	Q03304	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
DGG	1CQX	P39662	735.0 Da LogP 9.75 TPSA 148.8	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@…`
ECN	3OZV	P39662	381.7 Da LogP 5.80 TPSA 27.1	1 viol.	✓ Clean	`c1cc(ccc1COC(Cn2ccnc2)c3ccc(cc3Cl)Cl)Cl`
FDA	1TVC	P22868	787.6 Da LogP -1.75 TPSA 363.3	3 viol.	✓ Clean	`Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…`
FES	5OGX	A0A076MZ01	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
KKK	3OZW	P39662	531.4 Da LogP 4.21 TPSA 69.1	1 viol.	Alert	`CC(=O)N1CCN(CC1)c2ccc(cc2)OC[C@H]3CO[C@](O3)(Cn…`
X89	3OZU	P39662	416.1 Da LogP 6.45 TPSA 27.1	1 viol.	✓ Clean	`c1cc(c(cc1Cl)Cl)CO[C@@H](Cn2ccnc2)c3ccc(cc3Cl)Cl`

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
ZINC1615342	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC102191119	0.824	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@@H](O)CO…`
ZINC58649551	0.824	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](O)CO)…`
ZINC28568236	0.795	489.4 Da LogP 3.95 TPSA 60.8	✓ Ro5	Alert	`Clc1ccc([C@@]2(Cn3ccnc3)OC[C@H](COc3ccc(N4CCNCC…`
ZINC31416683	0.795	489.4 Da LogP 3.95 TPSA 60.8	✓ Ro5	Alert	`Clc1ccc([C@]2(Cn3ccnc3)OC[C@@H](COc3ccc(N4CCNCC…`
ZINC38944078	0.795	489.4 Da LogP 3.95 TPSA 60.8	✓ Ro5	Alert	`Clc1ccc([C@]2(Cn3ccnc3)OC[C@H](COc3ccc(N4CCNCC4…`
ZINC38944080	0.795	489.4 Da LogP 3.95 TPSA 60.8	✓ Ro5	Alert	`Clc1ccc([C@@]2(Cn3ccnc3)OC[C@@H](COc3ccc(N4CCNC…`
ZINC1532199	0.729	297.2 Da LogP 4.13 TPSA 27.1	✓ Ro5	✓ Clean	`C=CCO[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC1532200	0.729	297.2 Da LogP 4.13 TPSA 27.1	✓ Ro5	✓ Clean	`C=CCO[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC95918118	0.673	312.8 Da LogP 4.49 TPSA 27.1	✓ Ro5	✓ Clean	`Clc1ccc(CO[C@H](Cn2ccnc2)c2ccccc2)cc1`
ZINC95918119	0.673	312.8 Da LogP 4.49 TPSA 27.1	✓ Ro5	✓ Clean	`Clc1ccc(CO[C@@H](Cn2ccnc2)c2ccccc2)cc1`
ZINC102191158	0.660	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[C@…`
ZINC14880758	0.660	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OC[…`
ZINC14880760	0.660	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OC[C…`
ZINC53683910	0.660	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[…`
ZINC62592202	0.660	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[C@…`
ZINC62592203	0.660	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC[C…`
ZINC62592204	0.660	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC…`
ZINC96094841	0.660	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC[C…`
ZINC849188212	0.654	327.2 Da LogP 4.13 TPSA 44.1	✓ Ro5	✓ Clean	`CC(C)C(=O)O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC849188213	0.654	327.2 Da LogP 4.13 TPSA 44.1	✓ Ro5	✓ Clean	`CC(C)C(=O)O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC38334168	0.649	407.3 Da LogP 2.43 TPSA 79.7	✓ Ro5	✓ Clean	`CS(=O)(=O)OC[C@@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc…`
ZINC198375289	0.635	299.2 Da LogP 3.49 TPSA 44.1	✓ Ro5	✓ Clean	`CC(=O)O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC198375301	0.635	299.2 Da LogP 3.49 TPSA 44.1	✓ Ro5	✓ Clean	`CC(=O)O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC5349880	0.628	433.3 Da LogP 4.32 TPSA 62.6	✓ Ro5	✓ Clean	`O=C(OC[C@@H]1CO[C@@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O…`
ZINC5349883	0.628	433.3 Da LogP 4.32 TPSA 62.6	✓ Ro5	✓ Clean	`O=C(OC[C@H]1CO[C@@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1…`
ZINC638711	0.628	433.3 Da LogP 4.32 TPSA 62.6	✓ Ro5	✓ Clean	`O=C(OC[C@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1)…`
ZINC638717	0.628	433.3 Da LogP 4.32 TPSA 62.6	✓ Ro5	✓ Clean	`O=C(OC[C@@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1…`
ZINC297645	0.620	329.2 Da LogP 2.45 TPSA 56.5	✓ Ro5	✓ Clean	`OC[C@@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC297649	0.620	329.2 Da LogP 2.45 TPSA 56.5	✓ Ro5	✓ Clean	`OC[C@@H]1CO[C@@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC297652	0.620	329.2 Da LogP 2.45 TPSA 56.5	✓ Ro5	✓ Clean	`OC[C@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC297656	0.620	329.2 Da LogP 2.45 TPSA 56.5	✓ Ro5	✓ Clean	`OC[C@H]1CO[C@@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC102190506	0.614	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCCN)OC(=O)CC…`
ZINC102190512	0.614	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)C…`
ZINC4217243	0.605	367.2 Da LogP 3.11 TPSA 45.5	✓ Ro5	✓ Clean	`C#CCOC[C@H]1CO[C@](Cn2ccnc2)(c2ccc(Cl)cc2Cl)O1`
ZINC390893	0.604	257.1 Da LogP 2.92 TPSA 38.0	✓ Ro5	✓ Clean	`O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC390894	0.604	257.1 Da LogP 2.92 TPSA 38.0	✓ Ro5	✓ Clean	`O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC21988957	0.600	483.4 Da LogP 4.17 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@H]2CO[C@](Cn3ccnc3)(c3ccc(…`
ZINC22057057	0.600	483.4 Da LogP 4.17 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@@H]2CO[C@@](Cn3ccnc3)(c3cc…`
ZINC22057060	0.600	483.4 Da LogP 4.17 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@@H]2CO[C@](Cn3ccnc3)(c3ccc…`
ZINC6088320	0.600	483.4 Da LogP 4.17 TPSA 79.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@H]2CO[C@@](Cn3ccnc3)(c3ccc…`
ZINC849187659	0.600	325.2 Da LogP 3.88 TPSA 44.1	✓ Ro5	✓ Clean	`O=C(O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl)C1CC1`
ZINC849187660	0.600	325.2 Da LogP 3.88 TPSA 44.1	✓ Ro5	✓ Clean	`O=C(O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl)C1CC1`
ZINC27416437	0.596	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCCN)OC(=O)CCCCC`
ZINC33902364	0.596	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)CCC…`
ZINC36178999	0.593	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC36179002	0.593	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC849188227	0.589	341.2 Da LogP 4.52 TPSA 44.1	✓ Ro5	✓ Clean	`CC(C)CC(=O)O[C@@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC849188228	0.589	341.2 Da LogP 4.52 TPSA 44.1	✓ Ro5	✓ Clean	`CC(C)CC(=O)O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`
ZINC849188301	0.589	355.3 Da LogP 4.91 TPSA 44.1	✓ Ro5	✓ Clean	`CCC(CC)C(=O)O[C@H](Cn1ccnc1)c1ccc(Cl)cc1Cl`

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.