Protein profile

PA3128

short-chain dehydrogenase

Genome: NC_002516.2

Gene: PA3128 Structure source: Experimental + AlphaFold UniProt Q9HZ96

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Amino acids 248

Annotations 2

Features 29

PDB binders 21

Druggability 0.434

Overview

Basic information about this protein and its source genome.

Accession: PA3128
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA3128
Status: annotated
Amino acids: 248
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: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 (%): 40.23
Human E-value: 1.31e-10
Gut microbiome off-target: hit
Essential (DEG): Y
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 0.434

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 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: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.

29 records

Show feature table

Start	End	DB	Term	Name
1	12	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
29	248	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
24	28	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
13	23	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
2	248	Gene3D	G3DSA:3.40.50.720	-
212	232	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
212	232	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
157	176	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
157	176	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
79	90	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
79	90	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
4	21	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
4	21	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
130	146	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
130	146	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
178	195	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
178	195	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
136	144	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
136	144	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
157	176	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
79	90	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
30	50	Coils	Coil	Coil
9	247	Pfam	PF13561	Enoyl-(Acyl carrier protein) reductase
1	28	Phobius	SIGNAL_PEPTIDE	Signal peptide region
1	248	FunFam	G3DSA:3.40.50.720:FF:000084	Short-chain dehydrogenase reductase
4	247	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
4	247	InterPro	IPR036291	NAD(P)-binding domain superfamily
6	244	CDD	cd05233	SDR_c
3	248	PANTHER	PTHR43639	OXIDOREDUCTASE, SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY (AFU_ORTHOLOGUE AFUA_5G02870)

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 8BCJ	X-ray	1.15 Å	A,B,C,D	100.0% 1-248	PDBe RCSB PDBj File	Viewing
PDB 8BCI	X-ray	1.70 Å	A,B,C,D	100.0% 1-248	PDBe RCSB PDBj File	Loaded
AlphaFold PA3128	AlphaFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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	40.32	0.964
2	3.05	0.101
3	1.82	0.034

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
2				0.434
1				0.205

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.

71 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
2V4	4OSP	K0IB23	338.3 Da LogP 1.75 TPSA 111.9	✓ Ro5	Alert	`C[C@]1(Cc2cc(c3c(c2C(=O)C1)C(=O)c4cccc(c4C3=O)O…`
34X	4BO8	O54438	311.3 Da LogP 3.05 TPSA 85.0	✓ Ro5	✓ Clean	`c1ccc(cc1)c2cn(c(n2)N)NC(=O)Nc3ccccc3F`
36E	4BNT	O54438	186.1 Da LogP 2.58 TPSA 28.7	✓ Ro5	✓ Clean	`c1ccc2c(c1)[nH]c(n2)C(F)(F)F`
36G	4BO4	O54438	282.3 Da LogP 3.68 TPSA 41.6	✓ Ro5	✓ Clean	`COc1ccccc1NC(=O)N2CCCc3c2cccc3`
36I	4BNY	O54438	297.4 Da LogP 3.19 TPSA 38.2	✓ Ro5	✓ Clean	`c1ccc(cc1)c2nc3ccsc3c(n2)N4CCOCC4`
36K	4BO2	O54438	310.4 Da LogP 3.71 TPSA 68.2	✓ Ro5	✓ Clean	`CCn1c2ccccc2nc1NC(=O)Nc3ccccc3OC`
36P	4BO6	O54438	312.4 Da LogP 4.07 TPSA 33.2	✓ Ro5	✓ Clean	`c1ccc2c(c1)CCN2C(=O)c3csc(n3)c4ccsc4`
3X3	4BO9	O54438	318.3 Da LogP 3.50 TPSA 66.0	✓ Ro5	✓ Clean	`c1ccc(cc1)n2nc(nn2)c3ccccc3OCc4ccco4`
8M5	4BNZ	O54438	250.3 Da LogP 3.43 TPSA 34.0	✓ Ro5	✓ Clean	`Cn1cc(c2c1cccc2)C(=O)Nc3ccccc3`
9KQ	4BNU	O54438	273.3 Da LogP 2.88 TPSA 56.5	✓ Ro5	✓ Clean	`c1ccc(cc1)c2nc3ccccc3c(n2)n4cnnc4`
CAC	3I3O	A0A6L8PL20	137.0 Da LogP -0.52 TPSA 40.1	✓ Ro5	✓ Clean	`C[As](=O)(C)[O-]`
FXE	4BO0	O54438	326.4 Da LogP 3.23 TPSA 77.4	✓ Ro5	✓ Clean	`Cn1c2cccc(c2c(n1)NC(=O)Nc3ccccc3OC)OC`
J2T	4BO7	O54438	252.3 Da LogP 1.75 TPSA 68.0	✓ Ro5	✓ Clean	`c1cc2c(cc1Nc3ccc4nnnn4n3)CCC2`
NAE	3I3O	A0A6L8PL20	719.5 Da LogP -3.52 TPSA 338.2	3 viol.	✓ Clean	`CC(=O)Cc1cc[n+](cc1C(=O)N)[C@H]2[C@@H]([C@@H]([…`
NKH	4BO1	O54438	342.8 Da LogP 4.16 TPSA 60.5	✓ Ro5	✓ Clean	`COc1cc(c(cc1Cl)OC)NC(=O)c2cccc3c2nccc3`
O74	4BNX	O54438	347.8 Da LogP 4.53 TPSA 53.5	✓ Ro5	✓ Clean	`c1ccc2c(c1)C(=N/C(=C/3\C=CC=CC3=O)/N2)Nc4ccccc4…`
Q7U	4BNV	O54438	300.7 Da LogP 3.87 TPSA 59.0	✓ Ro5	✓ Clean	`Cn1c2ccccc2nc1NC(=O)Nc3ccccc3Cl`
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`
TCL	3OID	P71079	289.5 Da LogP 5.14 TPSA 29.5	1 viol.	✓ Clean	`c1cc(c(cc1Cl)O)Oc2ccc(cc2Cl)Cl`
U98	4BO3	O54438	317.3 Da LogP 2.49 TPSA 85.1	✓ Ro5	✓ Clean	`c1cc(cc(c1)Nc2c(cccn2)S(=O)(=O)N)C(F)(F)F`
WI4	4BO5	O54438	271.7 Da LogP 3.06 TPSA 55.6	✓ Ro5	✓ Clean	`c1ccc(c(c1)Nc2ncnc(n2)n3cccc3)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
ZINC13152723	1.000	310.4 Da LogP 3.71 TPSA 68.2	✓ Ro5	✓ Clean	`CCn1c(NC(=O)Nc2ccccc2OC)nc2ccccc21`
ZINC1399281	1.000	297.4 Da LogP 3.19 TPSA 38.2	✓ Ro5	✓ Clean	`c1ccc(-c2nc(N3CCOCC3)c3sccc3n2)cc1`
ZINC27923853	1.000	300.7 Da LogP 3.87 TPSA 59.0	✓ Ro5	✓ Clean	`Cn1c(NC(=O)Nc2ccccc2Cl)nc2ccccc21`
ZINC318945	1.000	282.3 Da LogP 3.68 TPSA 41.6	✓ Ro5	✓ Clean	`COc1ccccc1NC(=O)N1CCCc2ccccc21`
ZINC4654730	1.000	338.3 Da LogP 1.75 TPSA 111.9	✓ Ro5	Alert	`C[C@]1(O)CC(=O)c2c(cc(O)c3c2C(=O)c2cccc(O)c2C3=…`
ZINC481463	1.000	317.3 Da LogP 2.49 TPSA 85.1	✓ Ro5	✓ Clean	`NS(=O)(=O)c1cccnc1Nc1cccc(C(F)(F)F)c1`
ZINC6032158	1.000	338.3 Da LogP 1.75 TPSA 111.9	✓ Ro5	Alert	`C[C@@]1(O)CC(=O)c2c(cc(O)c3c2C(=O)c2cccc(O)c2C3…`
ZINC7913991	1.000	250.3 Da LogP 3.43 TPSA 34.0	✓ Ro5	✓ Clean	`Cn1cc(C(=O)Nc2ccccc2)c2ccccc21`
ZINC8231765	1.000	342.8 Da LogP 4.16 TPSA 60.5	✓ Ro5	✓ Clean	`COc1cc(NC(=O)c2cccc3cccnc23)c(OC)cc1Cl`
ZINC8429509	1.000	312.4 Da LogP 4.07 TPSA 33.2	✓ Ro5	✓ Clean	`O=C(c1csc(-c2ccsc2)n1)N1CCc2ccccc21`
ZINC8723457	1.000	252.3 Da LogP 1.75 TPSA 68.0	✓ Ro5	✓ Clean	`c1cc2c(cc1Nc1ccc3nnnn3n1)CCC2`
ZINC8726387	1.000	273.3 Da LogP 2.88 TPSA 56.5	✓ Ro5	✓ Clean	`c1ccc(-c2nc(-n3cnnc3)c3ccccc3n2)cc1`
ZINC89647	1.000	271.7 Da LogP 3.06 TPSA 55.6	✓ Ro5	✓ Clean	`Clc1ccccc1Nc1ncnc(-n2cccc2)n1`
ZINC9338279	1.000	311.3 Da LogP 3.05 TPSA 85.0	✓ Ro5	✓ Clean	`Nc1nc(-c2ccccc2)cn1NC(=O)Nc1ccccc1F`
ZINC451821	0.857	268.3 Da LogP 3.29 TPSA 41.6	✓ Ro5	✓ Clean	`COc1ccccc1NC(=O)N1CCc2ccccc21`
ZINC12534489	0.833	307.4 Da LogP 3.39 TPSA 63.1	✓ Ro5	✓ Clean	`CC(=O)Nc1ccc(NC(=O)c2cn(C)c3ccccc23)cc1`
ZINC27923895	0.833	335.2 Da LogP 4.52 TPSA 59.0	✓ Ro5	✓ Clean	`Cn1c(NC(=O)Nc2cccc(Cl)c2Cl)nc2ccccc21`
ZINC7917230	0.833	264.3 Da LogP 3.74 TPSA 34.0	✓ Ro5	✓ Clean	`Cc1ccc(NC(=O)c2cn(C)c3ccccc23)cc1`
ZINC32497089	0.811	278.3 Da LogP 2.79 TPSA 51.1	✓ Ro5	✓ Clean	`Cn1cc(C(=O)Nc2ccccc2)c(=O)c2ccccc21`
ZINC27923339	0.800	340.4 Da LogP 3.72 TPSA 77.4	✓ Ro5	✓ Clean	`CCn1c(NC(=O)Nc2cc(OC)ccc2OC)nc2ccccc21`
ZINC95453238	0.800	360.8 Da LogP 4.30 TPSA 60.5	✓ Ro5	✓ Clean	`COc1cc(NC(=O)c2cc(F)cc3cccnc23)c(OC)cc1Cl`
ZINC8074404	0.795	293.3 Da LogP 2.53 TPSA 77.1	✓ Ro5	✓ Clean	`Cn1cc(C(=O)Nc2ccc(C(N)=O)cc2)c2ccccc21`
ZINC32726013	0.789	251.3 Da LogP 2.83 TPSA 46.9	✓ Ro5	✓ Clean	`Cn1cc(C(=O)Nc2ccncc2)c2ccccc21`
ZINC15934558	0.787	312.4 Da LogP 3.69 TPSA 50.8	✓ Ro5	✓ Clean	`COc1ccc(OC)c(NC(=O)N2CCCc3ccccc32)c1`
ZINC15934559	0.787	312.4 Da LogP 3.69 TPSA 50.8	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)N2CCCc3ccccc32)c(OC)c1`
ZINC27923428	0.784	344.8 Da LogP 4.36 TPSA 68.2	✓ Ro5	✓ Clean	`CCn1c(NC(=O)Nc2cc(Cl)ccc2OC)nc2ccccc21`
ZINC5875060	0.780	281.4 Da LogP 3.96 TPSA 29.0	✓ Ro5	✓ Clean	`c1ccc(-c2nc(N3CCCC3)c3sccc3n2)cc1`
ZINC2027558	0.773	318.3 Da LogP 3.09 TPSA 79.3	✓ Ro5	✓ Clean	`O=S(=O)(O)c1cccnc1Nc1cccc(C(F)(F)F)c1`
ZINC16552269	0.771	296.4 Da LogP 3.99 TPSA 41.6	✓ Ro5	✓ Clean	`COc1ccccc1NC(=O)N1CCCc2cc(C)ccc21`
ZINC6726962	0.771	296.4 Da LogP 3.99 TPSA 41.6	✓ Ro5	✓ Clean	`COc1ccc(C)cc1NC(=O)N1CCCc2ccccc21`
ZINC12515506	0.769	307.4 Da LogP 3.39 TPSA 63.1	✓ Ro5	✓ Clean	`CC(=O)Nc1cccc(NC(=O)c2cn(C)c3ccccc23)c1`
ZINC15934557	0.766	296.4 Da LogP 4.07 TPSA 41.6	✓ Ro5	✓ Clean	`CCOc1ccccc1NC(=O)N1CCCc2ccccc21`
ZINC5903093	0.762	309.4 Da LogP 4.74 TPSA 29.0	✓ Ro5	✓ Clean	`c1ccc(-c2nc(N3CCCCCC3)c3sccc3n2)cc1`
ZINC27646798	0.761	313.4 Da LogP 2.90 TPSA 58.5	✓ Ro5	✓ Clean	`Oc1cccc(-c2nc(N3CCOCC3)c3sccc3n2)c1`
ZINC12537702	0.750	251.3 Da LogP 2.83 TPSA 46.9	✓ Ro5	✓ Clean	`Cn1cc(C(=O)Nc2cccnc2)c2ccccc21`
ZINC15517080	0.750	280.3 Da LogP 3.44 TPSA 43.3	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2cn(C)c3ccccc23)cc1`
ZINC238546717	0.750	247.0 Da LogP 3.01 TPSA 28.7	✓ Ro5	✓ Clean	`FC(F)(Br)c1nc2ccccc2[nH]1`
ZINC58201461	0.750	321.4 Da LogP 3.78 TPSA 63.1	✓ Ro5	✓ Clean	`CCC(=O)Nc1ccc(NC(=O)c2cn(C)c3ccccc23)cc1`
ZINC35585	0.745	327.2 Da LogP 3.66 TPSA 60.5	✓ Ro5	✓ Clean	`COc1cc(NC(=O)c2cccnc2Cl)c(OC)cc1Cl`
ZINC14139384	0.740	312.8 Da LogP 4.15 TPSA 51.2	✓ Ro5	✓ Clean	`COc1ccc(NC(=O)c2cccc3cccnc23)cc1Cl`
ZINC13572776	0.739	298.4 Da LogP 3.84 TPSA 24.5	✓ Ro5	✓ Clean	`COc1ccccc1NC(=S)N1CCCc2ccccc21`
ZINC27923561	0.739	328.8 Da LogP 4.74 TPSA 59.0	✓ Ro5	✓ Clean	`CCCn1c(NC(=O)Nc2ccccc2Cl)nc2ccccc21`
ZINC27924114	0.738	280.3 Da LogP 3.53 TPSA 59.0	✓ Ro5	✓ Clean	`Cc1ccccc1NC(=O)Nc1nc2ccccc2n1C`
ZINC4654724	0.738	322.3 Da LogP 2.05 TPSA 91.7	✓ Ro5	Alert	`C[C@@]1(O)CC(=O)c2c(ccc3c2C(=O)c2cccc(O)c2C3=O)…`
ZINC4654725	0.738	322.3 Da LogP 2.05 TPSA 91.7	✓ Ro5	Alert	`C[C@]1(O)CC(=O)c2c(ccc3c2C(=O)c2cccc(O)c2C3=O)C1`
ZINC10651406	0.735	295.3 Da LogP 3.32 TPSA 56.2	✓ Ro5	✓ Clean	`CCn1c(NC(=O)c2ccccc2OC)nc2ccccc21`
ZINC27923310	0.733	314.8 Da LogP 4.35 TPSA 59.0	✓ Ro5	✓ Clean	`CCn1c(NC(=O)Nc2ccccc2Cl)nc2ccccc21`
ZINC10550167	0.732	343.4 Da LogP 2.80 TPSA 80.2	✓ Ro5	✓ Clean	`Cn1cc(C(=O)Nc2ccc(NS(C)(=O)=O)cc2)c2ccccc21`
ZINC12552372	0.732	293.3 Da LogP 2.53 TPSA 77.1	✓ Ro5	✓ Clean	`Cn1cc(C(=O)Nc2cccc(C(N)=O)c2)c2ccccc21`
ZINC7941110	0.732	308.3 Da LogP 3.22 TPSA 60.3	✓ Ro5	✓ Clean	`COC(=O)c1ccc(NC(=O)c2cn(C)c3ccccc23)cc1`

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.