Protein profile

PA4098

short-chain dehydrogenase

Genome: NC_002516.2

Gene: PA4098 Structure source: Experimental + AlphaFold UniProt Q9HWT0

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Amino acids 241

Annotations 4

Features 25

PDB binders 12

Druggability 0.65

Overview

Basic information about this protein and its source genome.

Accession: PA4098
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4098
Status: annotated
Amino acids: 241
Structure source: Experimental + AlphaFold

GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP. GO:0030497 The elongation of a fatty acid chain by the sequential addition of two-carbon units. 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 (%): 41.406
Human E-value: 2.1e-16
Gut microbiome off-target: hit
Essential (DEG): N
Localization: Cytoplasmic

Selected Druggability evidence

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 0.65

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MVFQHDIYAGQQVLVTGGSSGIGAAIAMQFAELGAEVVALGLDADGVHAPRHPRIRREELDITDSQRLQRLFEALPRLDVLVNNAGISRDREEYDLATFERVLRLNLSAAMLASQLARPLLAQRGGSILNIASMYSTFGSADRPAYSASKGAIVQLTRSLACEYAAERIRVNAIAPGWIDTPLGAGLKADVEATRRIMQRTPLARWGEAPEVASAAAFLCGPGASFVTGAVLAVDGGYLCA

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
GO:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
GO:0030497 The elongation of a fatty acid chain by the sequential addition of two-carbon units.
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.

25 records

Show feature table

Start	End	DB	Term	Name
13	235	CDD	cd05233	SDR_c
76	87	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
76	87	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
126	134	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
126	134	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
146	165	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
146	165	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
202	222	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
202	222	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
146	165	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
167	184	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
167	184	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
76	87	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
120	136	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
120	136	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
12	29	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
12	29	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
9	238	PANTHER	PTHR42760	SHORT-CHAIN DEHYDROGENASES/REDUCTASES FAMILY MEMBER
1	241	Gene3D	G3DSA:3.40.50.720	-
10	239	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
10	239	InterPro	IPR036291	NAD(P)-binding domain superfamily
133	161	ProSitePatterns	PS00061	Short-chain dehydrogenases/reductases family signature.
133	161	InterPro	IPR020904	Short-chain dehydrogenase/reductase, conserved site
5	241	FunFam	G3DSA:3.40.50.720:FF:000084	Short-chain dehydrogenase reductase
19	238	Pfam	PF13561	Enoyl-(Acyl carrier protein) reductase

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

2 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 4B79	X-ray	1.98 Å	A,B	100.0% 1-241	PDBe RCSB PDBj File	Viewing
PDB 4AVY	X-ray	2.00 Å	A,B	100.0% 1-241	PDBe RCSB PDBj File	Loaded
AlphaFold PA4098	AlphaFold	—	—	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				0.65
5				0.32
2				0.305
3				0.205

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	7.03	0.364
2	4.99	0.226
3	1.42	0.018
4	1.37	0.016

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				0.742

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.

62 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
1SP	2WDZ	C0KTJ6	104.1 Da LogP 0.14 TPSA 40.5	✓ Ro5	✓ Clean	`CCC[C@@H](CO)O`
3HR	3VDR	D0VWQ0	104.1 Da LogP -0.16 TPSA 57.5	✓ Ro5	✓ Clean	`C[C@H](CC(=O)O)O`
5XC	5FFF	A0A1A9TAK5	150.1 Da LogP 1.23 TPSA 35.5	✓ Ro5	✓ Clean	`c1cc2c(cc1C=O)OCO2`
AAE	6ZZQ	A0A1E3M3N6	102.1 Da LogP 0.05 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CC(=O)O`
AEF	5FF9	A0A1A9TAK5	137.2 Da LogP 0.89 TPSA 46.2	✓ Ro5	✓ Clean	`c1cc(ccc1CCN)O`
DXX	3W8D	D0VWQ0	118.1 Da LogP -0.21 TPSA 74.6	✓ Ro5	✓ Clean	`CC(C(=O)O)C(=O)O`
MLA	3W8F	D0VWQ0	104.1 Da LogP -0.45 TPSA 74.6	✓ Ro5	✓ Clean	`C(C(=O)O)C(=O)O`
MRY	3LQF	C0KTJ6	122.1 Da LogP -2.31 TPSA 80.9	✓ Ro5	✓ Clean	`C([C@H]([C@H](CO)O)O)O`
POL	2WSB	C0KTJ6	60.1 Da LogP 0.39 TPSA 20.2	✓ Ro5	✓ Clean	`CCCO`
PTO	2AE2	P50163	141.2 Da LogP 0.60 TPSA 23.5	✓ Ro5	✓ Clean	`CN1[C@H]2CC[C@@H]1CC(C2)O`
QT8	6ZZS	A0A1E3M3N6	116.1 Da LogP 0.44 TPSA 54.4	✓ Ro5	✓ Clean	`CCC(=O)CC(=O)O`
TNE	1IPF	P50163	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
ZINC13681005	0.750	229.3 Da LogP 2.69 TPSA 55.5	✓ Ro5	✓ Clean	`NCCc1ccc(Oc2ccc(O)cc2)cc1`
ZINC8729752	0.724	226.2 Da LogP 2.89 TPSA 35.5	✓ Ro5	✓ Clean	`O=Cc1ccc(-c2ccc3c(c2)OCO3)cc1`
ZINC17877731	0.690	340.4 Da LogP 1.34 TPSA 72.5	✓ Ro5	✓ Clean	`O=Cc1ccc2c(c1)OCCOCCOCCOCCOCCO2`
ZINC4566282	0.690	416.4 Da LogP 2.57 TPSA 89.5	✓ Ro5	✓ Clean	`O=Cc1ccc2c(c1)OCCOCCOc1ccc(C=O)cc1OCCOCCO2`
ZINC4737459	0.690	416.4 Da LogP 2.57 TPSA 89.5	✓ Ro5	✓ Clean	`O=Cc1ccc2c(c1)OCCOCCOc1cc(C=O)ccc1OCCOCCO2`
ZINC4975920	0.690	296.3 Da LogP 1.32 TPSA 63.2	✓ Ro5	✓ Clean	`O=Cc1ccc2c(c1)OCCOCCOCCOCCO2`
ZINC74735	0.690	252.3 Da LogP 1.30 TPSA 54.0	✓ Ro5	✓ Clean	`O=Cc1ccc2c(c1)OCCOCCOCCO2`
ZINC1562031	0.684	214.3 Da LogP 2.88 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(CCc2ccc(O)cc2)cc1`
ZINC34925604	0.682	213.3 Da LogP 2.76 TPSA 46.2	✓ Ro5	Alert	`Nc1ccc(CCc2ccc(O)cc2)cc1`
ZINC33427554	0.656	226.2 Da LogP 2.89 TPSA 35.5	✓ Ro5	✓ Clean	`O=Cc1cccc(-c2ccc3c(c2)OCO3)c1`
ZINC2390999	0.655	275.3 Da LogP -1.99 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC47845246	0.625	227.3 Da LogP 3.15 TPSA 46.2	✓ Ro5	Alert	`Nc1ccc(CCCc2ccc(O)cc2)cc1`
ZINC1602323	0.621	296.3 Da LogP 2.60 TPSA 61.6	✓ Ro5	✓ Clean	`C(=N/N=C/c1ccc2c(c1)OCO2)\c1ccc2c(c1)OCO2`
ZINC17163879	0.621	296.3 Da LogP 2.60 TPSA 61.6	✓ Ro5	✓ Clean	`C(=N\N=C/c1ccc2c(c1)OCO2)\c1ccc2c(c1)OCO2`
ZINC8652404	0.621	296.3 Da LogP 2.60 TPSA 61.6	✓ Ro5	✓ Clean	`C(=N\N=C\c1ccc2c(c1)OCO2)\c1ccc2c(c1)OCO2`
ZINC1556073	0.619	228.3 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(CCCc2ccc(O)cc2)cc1`
ZINC1628112	0.619	202.3 Da LogP 2.87 TPSA 40.5	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@@H](O)CO`
ZINC1696911	0.619	230.4 Da LogP 3.65 TPSA 40.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@@H](O)CO`
ZINC2041985	0.619	202.3 Da LogP 2.87 TPSA 40.5	✓ Ro5	✓ Clean	`CCCCCCCCCC[C@H](O)CO`
ZINC2045232	0.619	230.4 Da LogP 3.65 TPSA 40.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[C@H](O)CO`
ZINC85479304	0.619	258.4 Da LogP 4.43 TPSA 40.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@H](O)CO`
ZINC85479307	0.619	258.4 Da LogP 4.43 TPSA 40.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC[C@@H](O)CO`
ZINC100055463	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC100064885	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC17780060	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC17952732	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC18042331	0.615	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H]…`
ZINC18120313	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC3979006	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC4403103	0.615	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC4403105	0.615	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC4403107	0.615	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@…`
ZINC9212412	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@@H](O)CO`
ZINC1405419	0.609	232.7 Da LogP 3.83 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1ccc(CCc2ccc(Cl)cc2)cc1`
ZINC13377961	0.594	322.3 Da LogP 3.44 TPSA 54.0	✓ Ro5	✓ Clean	`O=C(/C=C\c1ccc2c(c1)OCO2)/C=C\c1ccc2c(c1)OCO2`
ZINC152470	0.594	322.3 Da LogP 3.44 TPSA 54.0	✓ Ro5	✓ Clean	`O=C(/C=C/c1ccc2c(c1)OCO2)/C=C/c1ccc2c(c1)OCO2`
ZINC5698997	0.594	322.3 Da LogP 3.44 TPSA 54.0	✓ Ro5	✓ Clean	`O=C(/C=C\c1ccc2c(c1)OCO2)/C=C/c1ccc2c(c1)OCO2`
ZINC1556080	0.591	256.3 Da LogP 4.05 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(CCCCCc2ccc(O)cc2)cc1`
ZINC1842893	0.591	270.4 Da LogP 4.44 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(CCCCCCc2ccc(O)cc2)cc1`
ZINC3055005	0.591	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007	0.591	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010	0.591	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC38287274	0.588	328.5 Da LogP 2.75 TPSA 44.8	✓ Ro5	✓ Clean	`O=Cc1ccc2c(c1)OCCSCCOCCSCCO2`
ZINC584905809	0.588	294.4 Da LogP 0.47 TPSA 68.8	✓ Ro5	✓ Clean	`O=Cc1ccc2c(c1)OCCNCCOCCNCCO2`
ZINC2391099	0.586	274.3 Da LogP -2.59 TPSA 178.6	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)N[C@@H](CCC(N)=O)C(=O)O`
ZINC1649306	0.581	224.3 Da LogP 3.59 TPSA 18.5	✓ Ro5	✓ Clean	`C(=C/c1ccc2c(c1)OCO2)\c1ccccc1`
ZINC5104879	0.581	224.3 Da LogP 3.59 TPSA 18.5	✓ Ro5	✓ Clean	`C(=C\c1ccc2c(c1)OCO2)\c1ccccc1`
ZINC18062842	0.576	348.4 Da LogP 3.97 TPSA 54.0	✓ Ro5	Alert	`O=C1/C(=C\c2ccc3c(c2)OCO3)CC/C1=C\c1ccc2c(c1)OC…`
ZINC187289	0.576	348.4 Da LogP 3.97 TPSA 54.0	✓ Ro5	Alert	`O=C1/C(=C\c2ccc3c(c2)OCO3)CC/C1=C/c1ccc2c(c1)OC…`
ZINC4949646	0.576	348.4 Da LogP 3.97 TPSA 54.0	✓ Ro5	Alert	`O=C1/C(=C/c2ccc3c(c2)OCO3)CC/C1=C\c1ccc2c(c1)OC…`

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.