Protein profile

KP13_04520

2-halobenzoate 1,2-dioxygenase large subunit

Genome: KpKP13

Gene: AHE44396.1 cbdA Structure source: AlphaFold + ColabFold UniProt A0A0H3GNW3

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Amino acids 460

Annotations 4

Features 29

PDB binders 20

Druggability 0.294

Overview

Basic information about this protein and its source genome.

Accession: KP13_04520
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44396.1 cbdA
Status: annotated
Amino acids: 460
Structure source: AlphaFold + ColabFold

GO:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances. GO:0005506 Binding to an iron (Fe) ion. 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:0051213 Catalysis of the incorporation of both atoms of molecular oxygen (O2) into the substrate.

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: 94.65

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 0.294

Structure A0A0H3GNW3

Pocket Pocket 14

P2Rank 0.723

Structure A0A0H3GNW3

Pocket Pocket 1

ColabFold model

FPocket 0.392 · Pocket 4

P2Rank 0.629 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 29 / 4744 genomes with a hit

Normalized 0.006

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

GO:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances.
GO:0005506 Binding to an iron (Fe) ion.
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:0051213 Catalysis of the incorporation of both atoms of molecular oxygen (O2) into the substrate.

Sequence Features

Domain/signature hits from InterPro and related databases.

29 records

Show feature table

Start	End	DB	Term	Name
10	444	PANTHER	PTHR43756	CHOLINE MONOOXYGENASE, CHLOROPLASTIC
10	444	InterPro	IPR001663	Aromatic-ring-hydroxylating dioxygenase, alpha subunit
201	438	Pfam	PF00848	Ring hydroxylating alpha subunit (catalytic domain)
201	438	InterPro	IPR015879	Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain
49	132	Pfam	PF00355	Rieske [2Fe-2S] domain
49	132	InterPro	IPR017941	Rieske [2Fe-2S] iron-sulphur domain
34	59	PRINTS	PR00090	Ring hydroxylating dioxygenase alpha-subunit signature
34	59	InterPro	IPR001663	Aromatic-ring-hydroxylating dioxygenase, alpha subunit
85	105	PRINTS	PR00090	Ring hydroxylating dioxygenase alpha-subunit signature
85	105	InterPro	IPR001663	Aromatic-ring-hydroxylating dioxygenase, alpha subunit
106	126	PRINTS	PR00090	Ring hydroxylating dioxygenase alpha-subunit signature
106	126	InterPro	IPR001663	Aromatic-ring-hydroxylating dioxygenase, alpha subunit
152	178	PRINTS	PR00090	Ring hydroxylating dioxygenase alpha-subunit signature
152	178	InterPro	IPR001663	Aromatic-ring-hydroxylating dioxygenase, alpha subunit
193	215	PRINTS	PR00090	Ring hydroxylating dioxygenase alpha-subunit signature
193	215	InterPro	IPR001663	Aromatic-ring-hydroxylating dioxygenase, alpha subunit
64	79	PRINTS	PR00090	Ring hydroxylating dioxygenase alpha-subunit signature
64	79	InterPro	IPR001663	Aromatic-ring-hydroxylating dioxygenase, alpha subunit
14	167	SUPERFAMILY	SSF50022	ISP domain
14	167	InterPro	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily
49	176	Gene3D	G3DSA:2.102.10.10	-
49	176	InterPro	IPR036922	Rieske [2Fe-2S] iron-sulphur domain superfamily
92	115	ProSitePatterns	PS00570	Bacterial ring hydroxylating dioxygenases alpha-subunit signature.
92	115	InterPro	IPR015881	Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site
199	439	CDD	cd08879	RHO_alpha_C_AntDO-like
27	438	Gene3D	G3DSA:3.90.380.10	-
51	148	ProSiteProfiles	PS51296	Rieske [2Fe-2S] iron-sulfur domain profile.
51	148	InterPro	IPR017941	Rieske [2Fe-2S] iron-sulphur domain
168	455	SUPERFAMILY	SSF55961	Bet v1-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_A0A0H3GNW3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04520	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
14				0.294

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	13.06	0.673
2	4.74	0.209
3	3.59	0.134
4	2.94	0.094
5	2.23	0.055

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				0.392

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	11.69	0.621
2	4.4	0.185
3	2.95	0.095
4	2.19	0.053
5	1.59	0.025

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
15O	4HJL	P0A111	162.6 Da LogP 3.49 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc2c(c1)cccc2Cl`
16M	4HM2	P0A111	138.2 Da LogP 2.80 TPSA 0.0	✓ Ro5	✓ Clean	`CCSc1ccccc1`
16N	4HM4	P0A111	118.2 Da LogP 2.18 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc2c(c1)CCC2`
16Q	4HM6	P0A111	122.2 Da LogP 2.09 TPSA 9.2	✓ Ro5	✓ Clean	`CCOc1ccccc1`
16R	4HM8	P0A111	124.2 Da LogP 2.41 TPSA 0.0	✓ Ro5	✓ Clean	`CSc1ccccc1`
1ON	4HM1	P0A111	132.2 Da LogP 1.82 TPSA 17.1	✓ Ro5	✓ Clean	`c1ccc2c(c1)CCC2=O`
3NT	2HMO	P0A111	137.1 Da LogP 1.90 TPSA 43.1	✓ Ro5	✓ Clean	`Cc1cccc(c1)[N+](=O)[O-]`
AN3	2HMM	P0A111	178.2 Da LogP 3.99 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc2cc3ccccc3cc2c1`
BNL	2GBX	A2TC87	154.2 Da LogP 3.35 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc(cc1)c2ccccc2`
FES	2HMJ	P0A111	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
IAC	4HM0	P0A111	175.2 Da LogP 1.79 TPSA 53.1	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(c[nH]2)CC(=O)O`
IND	1EG9	P0A110	117.2 Da LogP 2.17 TPSA 15.8	✓ Ro5	✓ Clean	`c1ccc2c(c1)cc[nH]2`
MBN	3EN1	A5W4F2	92.1 Da LogP 2.00 TPSA 0.0	✓ Ro5	✓ Clean	`Cc1ccccc1`
NPY	1O7G	P0A110	128.2 Da LogP 2.84 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc2ccccc2c1`
OXY	2GBW	A2TC87	32.0 Da LogP 0.07 TPSA 34.1	✓ Ro5	✓ Clean	`O=O`
PE3	3EN1	A5W4F2	634.8 Da LogP -0.81 TPSA 160.5	2 viol.	✓ Clean	`C(COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO)O`
PEY	2HMK	P0A111	178.2 Da LogP 3.99 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc2c(c1)ccc3c2cccc3`
PYJ	4HM3	P0A111	106.2 Da LogP 2.25 TPSA 0.0	✓ Ro5	✓ Clean	`CCc1ccccc1`
SYN	4HM7	P0A111	104.2 Da LogP 2.33 TPSA 0.0	✓ Ro5	✓ Clean	`C=Cc1ccccc1`
UNU	4HKV	P0A111	121.1 Da LogP 0.79 TPSA 43.1	✓ Ro5	✓ Clean	`c1ccc(cc1)C(=O)N`

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
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1721417	0.900	208.3 Da LogP 3.48 TPSA 17.1	✓ Ro5	✓ Clean	`O=C1CCc2ccccc2-c2ccccc21`
ZINC3085979	0.842	253.3 Da LogP 1.85 TPSA 77.2	✓ Ro5	Alert	`NC(=O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC2985405	0.810	258.3 Da LogP 3.54 TPSA 27.7	✓ Ro5	✓ Clean	`CCOc1ccc(OCCOc2ccccc2)cc1`
ZINC82046450	0.808	213.2 Da LogP 3.57 TPSA 43.1	✓ Ro5	✓ Clean	`Cc1cccc(-c2cccc([N+](=O)[O-])c2)c1`
ZINC34506355	0.778	232.4 Da LogP 4.56 TPSA 0.0	✓ Ro5	✓ Clean	`CSc1ccc(Sc2ccccc2)cc1`
ZINC4701957	0.773	272.3 Da LogP 3.93 TPSA 27.7	✓ Ro5	✓ Clean	`CCOc1ccc(OCCCOc2ccccc2)cc1`
ZINC1532617	0.767	203.2 Da LogP 1.36 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(O)C(=O)Cc1c[nH]c2ccccc12`
ZINC84689016	0.767	203.2 Da LogP 1.16 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(O)Cc1c[nH]c2ccccc2c1=O`
ZINC1653862	0.727	214.3 Da LogP 4.47 TPSA 0.0	✓ Ro5	✓ Clean	`CCSc1ccc(-c2ccccc2)cc1`
ZINC1681580	0.714	208.3 Da LogP 3.02 TPSA 17.1	✓ Ro5	✓ Clean	`O=C1c2ccccc2CCc2ccccc21`
ZINC1742206	0.714	208.3 Da LogP 3.57 TPSA 0.0	✓ Ro5	✓ Clean	`c1ccc2c(c1)CCc1ccccc1CC2`
ZINC3848035	0.714	236.3 Da LogP 2.85 TPSA 34.1	✓ Ro5	Alert	`O=C1C(=O)c2ccccc2CCc2ccccc21`
ZINC2984940	0.708	258.3 Da LogP 3.54 TPSA 27.7	✓ Ro5	✓ Clean	`CCOc1cccc(OCCOc2ccccc2)c1`
ZINC2985329	0.708	302.4 Da LogP 3.56 TPSA 36.9	✓ Ro5	✓ Clean	`CCOc1ccc(OCCOCCOc2ccccc2)cc1`
ZINC57380	0.706	232.2 Da LogP 0.91 TPSA 82.2	✓ Ro5	✓ Clean	`O=C(O)CNC(=O)Cc1c[nH]c2ccccc12`
ZINC141670423	0.700	229.2 Da LogP 3.70 TPSA 52.4	✓ Ro5	✓ Clean	`Cc1cccc(Oc2cccc([N+](=O)[O-])c2)c1`
ZINC205262	0.697	264.3 Da LogP 3.03 TPSA 44.9	✓ Ro5	✓ Clean	`O=C(Cc1c[nH]c2ccccc12)NCc1ccccc1`
ZINC57378	0.697	203.2 Da LogP 2.58 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)CCCc1c[nH]c2ccccc12`
ZINC1629403	0.696	222.3 Da LogP 3.21 TPSA 17.1	✓ Ro5	✓ Clean	`O=C1Cc2ccccc2CCc2ccccc21`
ZINC115086873	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1690614	0.688	233.2 Da LogP 1.50 TPSA 90.4	✓ Ro5	✓ Clean	`O=C(O)C(Cc1c[nH]c2ccccc12)C(=O)O`
ZINC1857792028	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC47212123	0.684	200.3 Da LogP 4.08 TPSA 0.0	✓ Ro5	✓ Clean	`CSc1ccc(-c2ccccc2)cc1`
ZINC2991309	0.680	272.3 Da LogP 3.93 TPSA 27.7	✓ Ro5	✓ Clean	`CCOc1cccc(OCCCOc2ccccc2)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.