Protein profile

KP13_03692

3-oxosteroid 1-dehydrogenase

Genome: KpKP13

Gene: ksdD AHE46029.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GSP8

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Amino acids 558

Annotations 2

Features 20

PDB binders 6

Druggability 0.466

Overview

Basic information about this protein and its source genome.

Accession: KP13_03692
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ksdD AHE46029.1
Status: annotated
Amino acids: 558
Structure source: AlphaFold + ColabFold

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:0008202 The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.

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: CytoplasmicMembrane
ColabFold pLDDT: 95.98

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 0.466

Structure A0A0H3GSP8

Pocket Pocket 31

P2Rank 0.959

Structure A0A0H3GSP8

Pocket Pocket 1

ColabFold model

FPocket 0.999 · Pocket 2

P2Rank 0.985 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 16 / 4744 genomes with a hit

Normalized 0.003

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

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:0008202 The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
1	5	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
419	554	Gene3D	G3DSA:3.50.50.60	-
419	554	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
1	379	Gene3D	G3DSA:3.50.50.60	-
1	379	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
23	558	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
337	493	SUPERFAMILY	SSF56425	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain
337	493	InterPro	IPR027477	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily
6	17	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	531	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
1	531	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
18	22	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	23	ProSiteProfiles	PS51257	Prokaryotic membrane lipoprotein lipid attachment site profile.
7	29	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
5	27	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
513	528	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
5	538	Pfam	PF00890	FAD binding domain
5	538	InterPro	IPR003953	FAD-dependent oxidoreductase 2, FAD binding domain
4	556	PANTHER	PTHR43400	FUMARATE REDUCTASE
1	22	Phobius	SIGNAL_PEPTIDE	Signal peptide region

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_A0A0H3GSP8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03692	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
31				0.466
1				0.297
20				0.0

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	45.44	0.959
2	7.07	0.307
3	6.73	0.289
4	4.76	0.173
5	3.93	0.126

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				0.999
30				0.613

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	19.52	0.84
2	13.18	0.677
3	8.73	0.467
4	2.99	0.097
5	2.94	0.095

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.

56 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
ANB	4C3Y	Q9RA02	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12CC[C@H]3[C@H]([C@@H]1CCC2=O)CCC4=CC(=O)C…`
ASD	4AT2	Q0S4Q9	286.4 Da LogP 4.09 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12CCC(=O)C=C1CC[C@@H]3[C@@H]2CC[C@]4([C@H]…`
FUM	1E39	P0C278	116.1 Da LogP -0.29 TPSA 74.6	✓ Ro5	✓ Clean	`C(=C/C(=O)O)\C(=O)O`
MEZ	1Y0P	P0C278	130.1 Da LogP 0.10 TPSA 74.6	✓ Ro5	✓ Clean	`C/C(=C\C(=O)O)/C(=O)O`
SIN	1D4D	P83223	118.1 Da LogP -0.06 TPSA 74.6	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)O`
TEO	1P2H	P0C278	132.1 Da LogP -3.14 TPSA 103.7	✓ Ro5	✓ Clean	`C(=C(\O)/[O-])\[C@H](C(=O)[O-])O`

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
ZINC156796	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@@]2(C)C…`
ZINC2100022	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@@]2(C)C…`
ZINC242548813	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@H]1[C@H]2CC[C@]2(C)C(=O…`
ZINC253502176	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@H](CCC4=CC(=O)C=C[C@]43C)[C@…`
ZINC3881421	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@]2(C)C(…`
ZINC4023563	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@@H](CCC4=CC(=O)C=C[C@@]43C)[…`
ZINC4023564	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@H]2CC[C@]2(C)C(=…`
ZINC4023565	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@]2(C)C(…`
ZINC4534007	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@@]12C=CC(=O)C=C1CC[C@H]1[C@H]2CC[C@@]2(C)C(…`
ZINC58482279	1.000	284.4 Da LogP 3.86 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@H]1[C@H]2CC[C@@]2(C)C(=…`
ZINC253499744	0.791	282.4 Da LogP 4.85 TPSA 17.1	✓ Ro5	✓ Clean	`C=C1C=C[C@@]2(C)C(=C1)CC[C@@H]1[C@H]2CC[C@]2(C)…`
ZINC253499746	0.791	282.4 Da LogP 4.85 TPSA 17.1	✓ Ro5	✓ Clean	`C=C1C=C[C@@]2(C)C(=C1)CC[C@@H]1[C@@H]2CC[C@]2(C…`
ZINC4024379	0.791	282.4 Da LogP 4.85 TPSA 17.1	✓ Ro5	✓ Clean	`C=C1C=C[C@@]2(C)C(=C1)CC[C@H]1[C@@H]3CCC(=O)[C@…`
ZINC4024380	0.791	282.4 Da LogP 4.85 TPSA 17.1	✓ Ro5	✓ Clean	`C=C1C=C[C@@]2(C)C(=C1)CC[C@@H]1[C@@H]2CC[C@]2(C…`
ZINC253617340	0.767	286.4 Da LogP 2.59 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@@H](CCC4=CC(=O)C=C[C@@]43O)[…`
ZINC253617341	0.767	286.4 Da LogP 2.59 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@H](CCC4=CC(=O)C=C[C@@]43O)[C…`
ZINC4292864	0.767	286.4 Da LogP 2.59 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@H](CCC4=CC(=O)C=C[C@@]43O)[C…`
ZINC4292866	0.767	286.4 Da LogP 2.59 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@@H](CCC4=CC(=O)C=C[C@@]43O)[…`
ZINC2386384549	0.727	304.8 Da LogP 3.83 TPSA 34.1	✓ Ro5	✓ Clean	`C[C@]12CC[C@H]3[C@@H](CCC4=CC(=O)C=C[C@@]43Cl)[…`
ZINC13513686	0.674	300.4 Da LogP 2.83 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@]12C[C@H](O)[C@H]3[C@@H](CCC4=CC(=O)C=C[C@@…`
ZINC1730510	0.674	298.4 Da LogP 3.04 TPSA 51.2	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2C(=O)C[C@@]2…`
ZINC1857623168	0.674	298.4 Da LogP 3.04 TPSA 51.2	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2C(=O)C[C@@]2…`
ZINC1857623169	0.674	298.4 Da LogP 3.04 TPSA 51.2	✓ Ro5	✓ Clean	`C[C@]12CC(=O)[C@H]3[C@@H](CCC4=CC(=O)C=C[C@@]43…`
ZINC254071261	0.674	298.4 Da LogP 3.04 TPSA 51.2	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@H]1[C@H]2C(=O)C[C@@]2(C…`
ZINC254071263	0.674	298.4 Da LogP 3.04 TPSA 51.2	✓ Ro5	✓ Clean	`C[C@]12CC(=O)[C@@H]3[C@H](CCC4=CC(=O)C=C[C@@]43…`
ZINC254071265	0.674	298.4 Da LogP 3.04 TPSA 51.2	✓ Ro5	✓ Clean	`C[C@@]12C=CC(=O)C=C1CC[C@H]1[C@H]2C(=O)C[C@]2(C…`
ZINC4533967	0.674	298.4 Da LogP 3.04 TPSA 51.2	✓ Ro5	✓ Clean	`C[C@@]12C=CC(=O)C=C1CC[C@H]1[C@H]2C(=O)C[C@@]2(…`
ZINC4706361	0.674	300.4 Da LogP 2.83 TPSA 54.4	✓ Ro5	✓ Clean	`C[C@]12C[C@@H](O)[C@H]3[C@@H](CCC4=CC(=O)C=C[C@…`
ZINC4897138	0.674	298.4 Da LogP 3.04 TPSA 51.2	✓ Ro5	✓ Clean	`C[C@]12CC(=O)[C@H]3[C@@H](CCC4=CC(=O)C=C[C@@]43…`
ZINC31623358	0.673	328.4 Da LogP 3.16 TPSA 60.4	✓ Ro5	✓ Clean	`CC(=O)O[C@]12C=CC(=O)C=C1CC[C@H]1[C@@H]3CCC(=O)…`
ZINC118912522	0.667	300.4 Da LogP 4.05 TPSA 37.3	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@@]2(C)[…`
ZINC3875469	0.667	300.4 Da LogP 4.05 TPSA 37.3	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@@]2(C)[…`
ZINC4023051	0.667	300.4 Da LogP 4.05 TPSA 37.3	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@H]1[C@@H]3CC[C@](C)(O)[…`
ZINC4023052	0.667	300.4 Da LogP 4.05 TPSA 37.3	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@H]2CC[C@@]2(C)[C…`
ZINC4023053	0.667	300.4 Da LogP 4.05 TPSA 37.3	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@@]2(C)[…`
ZINC105025894	0.660	300.4 Da LogP 3.59 TPSA 43.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@H](CCC4=CC(=O)C=C[C@@]43C)[C…`
ZINC11592582	0.660	300.4 Da LogP 3.59 TPSA 43.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@H]3[C@@H](CCC4=CC(=O)C=C[C@]43C)[C@…`
ZINC3831512	0.660	300.4 Da LogP 3.59 TPSA 43.4	✓ Ro5	✓ Clean	`C[C@@]12CC[C@@H]3[C@H](CCC4=CC(=O)C=C[C@]43C)[C…`
ZINC3831513	0.660	300.4 Da LogP 3.59 TPSA 43.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@H](CCC4=CC(=O)C=C[C@]43C)[C@…`
ZINC3831514	0.660	300.4 Da LogP 3.59 TPSA 43.4	✓ Ro5	✓ Clean	`C[C@@]12CC[C@H]3[C@H](CCC4=CC(=O)C=C[C@]43C)[C@…`
ZINC3831515	0.660	300.4 Da LogP 3.59 TPSA 43.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@H]3[C@H](CCC4=CC(=O)C=C[C@]43C)[C@@…`
ZINC4081770	0.660	300.4 Da LogP 3.59 TPSA 43.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@@H](CCC4=CC(=O)C=C[C@@]43C)[…`
ZINC4081771	0.660	300.4 Da LogP 3.59 TPSA 43.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@H]3[C@@H](CCC4=CC(=O)C=C[C@@]43C)[C…`
ZINC4081773	0.660	300.4 Da LogP 3.59 TPSA 43.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@@H](CCC4=CC(=O)C=C[C@@]43C)[…`
ZINC4081774	0.660	300.4 Da LogP 3.59 TPSA 43.4	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@]2(C)OC…`
ZINC5529977	0.660	300.4 Da LogP 3.59 TPSA 43.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@H](CCC4=CC(=O)C=C[C@@]43C)[C…`
ZINC5530039	0.660	300.4 Da LogP 3.59 TPSA 43.4	✓ Ro5	✓ Clean	`C[C@]12CC[C@H]3[C@H](CCC4=CC(=O)C=C[C@@]43C)[C@…`
ZINC253618127	0.652	286.4 Da LogP 3.66 TPSA 37.3	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1CC[C@@H]1[C@@H]2CC[C@@]2(C)[…`
ZINC97975660	0.652	298.4 Da LogP 3.04 TPSA 51.2	✓ Ro5	✓ Clean	`C[C@]12CC[C@@H]3[C@@H](CC(=O)C4=CC(=O)C=C[C@@]4…`
ZINC97975661	0.652	298.4 Da LogP 3.04 TPSA 51.2	✓ Ro5	✓ Clean	`C[C@]12C=CC(=O)C=C1C(=O)C[C@@H]1[C@H]2CC[C@]2(C…`

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.