Protein profile

KP13_03396

2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase

Genome: KpKP13

Gene: AHE45774.1 entA Structure source: AlphaFold + ColabFold UniProt A0A0H3GPR7

Export view

Amino acids 251

Annotations 4

Features 31

PDB binders 7

Druggability 0.876

Overview

Basic information about this protein and its source genome.

Accession: KP13_03396
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45774.1 entA
Status: annotated
Amino acids: 251
Structure source: AlphaFold + ColabFold

1.3.1.28

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. GO:0019290 The chemical reactions and pathways resulting in the formation of siderophores, low molecular weight Fe(III)-chelating substances made by aerobic or facultatively anaerobic bacteria, especially when growing under iron deficient conditions. The complexes of Fe(3+)-siderophores have very high stability constants and are taken up by specific transport systems by microorganisms; the subsequent release of iron requires enzymatic action. GO:0008667 Catalysis of the reaction: (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + NAD+ = 2,3-dihydroxybenzoate + H+ + NADH.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 34.058
Human E-value: 1.58e-15
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.35

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 0.876

Structure A0A0H3GPR7

Pocket Pocket 1

P2Rank 0.914

Structure A0A0H3GPR7

Pocket Pocket 1

ColabFold model

FPocket 0.892 · Pocket 1

P2Rank 0.883 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 84 / 4744 genomes with a hit

Normalized 0.018

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1.3.1.28

Gene Ontology (GO)

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.
GO:0019290 The chemical reactions and pathways resulting in the formation of siderophores, low molecular weight Fe(III)-chelating substances made by aerobic or facultatively anaerobic bacteria, especially when growing under iron deficient conditions. The complexes of Fe(3+)-siderophores have very high stability constants and are taken up by specific transport systems by microorganisms; the subsequent release of iron requires enzymatic action.
GO:0008667 Catalysis of the reaction: (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + NAD+ = 2,3-dihydroxybenzoate + H+ + NADH.

Sequence Features

Domain/signature hits from InterPro and related databases.

31 records

Show feature table

Start	End	DB	Term	Name
1	249	FunFam	G3DSA:3.40.50.720:FF:000160	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
9	180	SMART	SM00822	This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group.
15	248	Pfam	PF13561	Enoyl-(Acyl carrier protein) reductase
3	248	PANTHER	PTHR24321	DEHYDROGENASES, SHORT CHAIN
2	250	Gene3D	G3DSA:3.40.50.720	-
134	162	ProSitePatterns	PS00061	Short-chain dehydrogenases/reductases family signature.
134	162	InterPro	IPR020904	Short-chain dehydrogenase/reductase, conserved site
127	135	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
127	135	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
74	85	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
74	85	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
147	166	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
147	166	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
4	248	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
4	248	InterPro	IPR036291	NAD(P)-binding domain superfamily
11	251	CDD	cd05331	DH-DHB-DH_SDR_c
11	251	InterPro	IPR003560	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
15	32	PRINTS	PR01397	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature
15	32	InterPro	IPR003560	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
162	185	PRINTS	PR01397	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature
162	185	InterPro	IPR003560	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
201	220	PRINTS	PR01397	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature
201	220	InterPro	IPR003560	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
97	117	PRINTS	PR01397	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature
97	117	InterPro	IPR003560	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
77	94	PRINTS	PR01397	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature
77	94	InterPro	IPR003560	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
227	246	PRINTS	PR01397	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature
227	246	InterPro	IPR003560	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
11	250	NCBIfam	TIGR04316	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
11	250	InterPro	IPR003560	2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase

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...

Legend High Medium Low

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_A0A0H3GPR7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03396	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				0.876

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				15.48	0.754
2				3.02	0.099

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				0.892
22				0.531

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	15.26	0.75
2	3.91	0.154
3	3.04	0.101

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
A6O	6IHH	C0IR58	314.4 Da LogP 3.93 TPSA 46.5	✓ Ro5	✓ Clean	`CC[C@]1([C@H](CCC1=O)O)C/C=C/2\CCCc3c2ccc(c3)OC`
BUO	5OJG	G5EGA6	86.1 Da LogP 0.16 TPSA 34.1	✓ Ro5	Alert	`CC(=O)C(=O)C`
ISN	5OJI	G5EGA6	147.1 Da LogP 0.82 TPSA 46.2	✓ Ro5	✓ Clean	`c1ccc2c(c1)C(=O)C(=O)N2`
RM4	7DO7	C1DMX5	164.2 Da LogP -2.19 TPSA 90.2	✓ Ro5	✓ Clean	`C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O)O)O)O`
TAM	4BMN	C0IR58	163.2 Da LogP -1.17 TPSA 86.7	✓ Ro5	✓ Clean	`C(CO)C(CCO)(CCO)N`
TLA	5U9P	B4EEX4	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@@H]([C@H](C(=O)O)O)(C(=O)O)O`
TNE	1XHL	Q19774	139.2 Da LogP 0.81 TPSA 20.3	✓ Ro5	✓ Clean	`CN1[C@H]2CC[C@@H]1CC(=O)C2`

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
ZINC16974563	0.727	238.2 Da LogP 2.50 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2C(=O)Nc2ccccc21`
ZINC12359024	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC13533920	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1532740	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC1549593	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC2013424	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)C(=O)O`
ZINC3581021	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC3860635	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C(=O)O`
ZINC5783661	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)C(=O)O`
ZINC6072527	0.692	210.1 Da LogP -3.40 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)C(=O)O`
ZINC1845623	0.673	312.4 Da LogP 4.13 TPSA 43.4	✓ Ro5	✓ Clean	`CCC1(C/C=C2\CCCc3cc(OC)ccc32)C(=O)CCC1=O`
ZINC1845624	0.673	312.4 Da LogP 4.13 TPSA 43.4	✓ Ro5	✓ Clean	`CCC1(C/C=C2/CCCc3cc(OC)ccc32)C(=O)CCC1=O`
ZINC100014196	0.667	262.3 Da LogP 2.81 TPSA 58.2	✓ Ro5	Alert	`O=C1/C(=C2\Nc3ccccc3C2=O)Nc2ccccc21`
ZINC100513617	0.667	262.3 Da LogP 2.81 TPSA 58.2	✓ Ro5	Alert	`O=C1/C(=C2/Nc3ccccc3C2=O)Nc2ccccc21`
ZINC1857776489	0.667	262.3 Da LogP 2.81 TPSA 58.2	✓ Ro5	Alert	`O=C1C(=C2Nc3ccccc3C2=O)Nc2ccccc21`
ZINC3126818	0.667	210.2 Da LogP 3.00 TPSA 41.1	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2Nc2ccccc21`
ZINC32915988	0.667	262.3 Da LogP 2.50 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2/C1=C1\C(=O)Nc2ccccc21`
ZINC34172946	0.667	262.3 Da LogP 2.50 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2/C1=C1/C(=O)Nc2ccccc21`
ZINC45069786	0.667	271.3 Da LogP 4.59 TPSA 29.1	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2-c2ccccc2-c2ccccc21`
ZINC6117582	0.667	262.3 Da LogP 2.50 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2C1=C1C(=O)Nc2ccccc21`
ZINC401273	0.652	238.2 Da LogP 2.50 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2NC(=O)c2ccccc21`
ZINC100015416	0.643	262.3 Da LogP 2.66 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2/C1=C1\Nc2ccccc2C1=O`
ZINC1857626905	0.643	262.3 Da LogP 2.66 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2C1=C1Nc2ccccc2C1=O`
ZINC18825333	0.643	262.3 Da LogP 2.66 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2/C1=C1/Nc2ccccc2C1=O`
ZINC2575038	0.625	205.3 Da LogP 0.00 TPSA 86.7	✓ Ro5	✓ Clean	`NC(CCCO)(CCCO)CCCO`
ZINC117753192	0.600	203.2 Da LogP 1.65 TPSA 66.4	✓ Ro5	✓ Clean	`C/C(O)=C1\C(=O)Nc2ccccc2C1=O`
ZINC257166	0.593	290.3 Da LogP 1.78 TPSA 82.9	✓ Ro5	Alert	`O=C1Nc2ccccc2/C1=N\N=C1\C(=O)Nc2ccccc21`
ZINC1560405156	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(\O)[C@H](O)[C@H](O)C(=O)O`
ZINC1560405157	0.588	208.1 Da LogP -1.79 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)/C(O)=C(/O)[C@H](O)[C@H](O)C(=O)O`
ZINC85775	0.583	210.2 Da LogP 3.31 TPSA 41.1	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2-c2ccccc2N1`
ZINC3023696	0.571	257.2 Da LogP -0.24 TPSA 104.4	✓ Ro5	✓ Clean	`O=C1NC(=O)C(=C2C(=O)Nc3ccccc32)C(=O)N1`
ZINC36610867	0.571	446.4 Da LogP 3.32 TPSA 116.4	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2/C1=C1\C(=O)Nc2cc3c(cc21)NC(=O)/C3…`
ZINC16948211	0.567	223.2 Da LogP 2.49 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1Nc2ccc(-c3ccccc3)cc2C1=O`
ZINC35086915	0.567	223.2 Da LogP 2.49 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1Nc2cc(-c3ccccc3)ccc2C1=O`
ZINC16946250	0.563	257.7 Da LogP 3.14 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1Nc2ccc(-c3ccccc3Cl)cc2C1=O`
ZINC4644305	0.552	277.3 Da LogP 2.41 TPSA 70.2	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2N/C1=C1\C(=O)Nc2ccccc21`
ZINC16946233	0.545	237.3 Da LogP 2.80 TPSA 46.2	✓ Ro5	✓ Clean	`Cc1ccccc1-c1ccc2c(c1)C(=O)C(=O)N2`
ZINC16948184	0.545	241.2 Da LogP 2.63 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1Nc2ccc(-c3ccccc3F)cc2C1=O`
ZINC1662285	0.544	284.4 Da LogP 3.35 TPSA 43.4	✓ Ro5	✓ Clean	`COc1ccc2c(c1)CC/C2=C\CC1(C)C(=O)CCC1=O`
ZINC17380200	0.544	284.4 Da LogP 3.35 TPSA 43.4	✓ Ro5	✓ Clean	`COc1ccc2c(c1)CC/C2=C/CC1(C)C(=O)CCC1=O`
ZINC145153554	0.538	203.3 Da LogP 0.14 TPSA 54.5	✓ Ro5	✓ Clean	`CS(=O)(=O)N1[C@H]2CC[C@H]1CC(=O)C2`
ZINC101528567	0.533	205.2 Da LogP 0.99 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)/C(O)=C1/C(=O)Nc2ccccc21`
ZINC104097396	0.533	205.2 Da LogP 0.99 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)/C(O)=C1\C(=O)Nc2ccccc21`
ZINC1735953	0.531	224.3 Da LogP 3.30 TPSA 41.1	✓ Ro5	✓ Clean	`Cc1ccc2c(c1)Nc1ccccc1C(=O)N2`
ZINC63298372	0.531	224.3 Da LogP 3.30 TPSA 41.1	✓ Ro5	✓ Clean	`Cc1ccc2c(c1)NC(=O)c1ccccc1N2`
ZINC107464785	0.529	264.3 Da LogP 2.82 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2C(=O)/C1=C\Nc1ccccc1`
ZINC1661289	0.517	226.0 Da LogP 1.58 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1Nc2cc(Br)ccc2C1=O`
ZINC223812065	0.517	305.3 Da LogP 1.91 TPSA 87.3	✓ Ro5	✓ Clean	`O=C1NC(=O)C(=C2c3ccccc3Nc3ccccc32)C(=O)N1`
ZINC5945548	0.517	273.0 Da LogP 1.43 TPSA 46.2	✓ Ro5	✓ Clean	`O=C1Nc2cc(I)ccc2C1=O`
ZINC5948252	0.517	221.3 Da LogP 3.42 TPSA 29.1	✓ Ro5	✓ Clean	`O=C1Nc2ccccc2C=Cc2ccccc21`

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.