Protein profile

KP13_03439

Serine 3-dehydrogenase

Genome: KpKP13

Gene: AHE45815.1 sdh Structure source: AlphaFold + ColabFold UniProt A0A0H3GTM0

Export view

Amino acids 248

Annotations 2

Features 21

PDB binders 6

Druggability 0.918

Overview

Basic information about this protein and its source genome.

Accession: KP13_03439
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45815.1 sdh
Status: annotated
Amino acids: 248
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: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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 43.478
Human E-value: 7.57e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 49.194
DEG E-value: 1.19e-83
Localization: Cytoplasmic
ColabFold pLDDT: 98.28

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 0.918

Structure A0A0H3GTM0

Pocket Pocket 5

P2Rank 0.959

Structure A0A0H3GTM0

Pocket Pocket 1

ColabFold model

FPocket 0.417 · Pocket 1

P2Rank 0.962 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 97 / 4744 genomes with a hit

Normalized 0.02

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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
2	241	PANTHER	PTHR42901	ALCOHOL DEHYDROGENASE
148	167	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
148	167	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
73	84	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
73	84	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
128	136	PRINTS	PR00080	Short-chain dehydrogenase/reductase (SDR) superfamily signature
128	136	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
2	186	Pfam	PF00106	short chain dehydrogenase
2	186	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
135	163	ProSitePatterns	PS00061	Short-chain dehydrogenases/reductases family signature.
135	163	InterPro	IPR020904	Short-chain dehydrogenase/reductase, conserved site
1	238	FunFam	G3DSA:3.40.50.720:FF:000047	NADP-dependent L-serine/L-allo-threonine dehydrogenase
1	248	Gene3D	G3DSA:3.40.50.720	-
148	167	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
73	84	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
169	186	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
169	186	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
122	138	PRINTS	PR00081	Glucose/ribitol dehydrogenase family signature
122	138	InterPro	IPR002347	Short-chain dehydrogenase/reductase SDR
2	229	SUPERFAMILY	SSF51735	NAD(P)-binding Rossmann-fold domains
2	229	InterPro	IPR036291	NAD(P)-binding domain superfamily

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_A0A0H3GTM0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03439	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
5				0.918

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				31.91	0.941

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				0.417

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				32.52	0.944

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.

64 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
8X3	6IXJ	D3U1D9	126.1 Da LogP -1.13 TPSA 74.6	✓ Ro5	✓ Clean	`C(CS(=O)(=O)O)O`
AC0	1ZK1	Q84EX5	120.2 Da LogP 1.89 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccccc1`
ADE	1YXM	Q9BY49	135.1 Da LogP -0.06 TPSA 80.5	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)c(ncn2)N`
P4C	3EZL	Q3JRS9	324.4 Da LogP -0.72 TPSA 92.7	✓ Ro5	✓ Clean	`C(COCCOCCOCCOCCOCCOCC=O)O`
SS2	1ZJY	Q84EX5	122.2 Da LogP 1.74 TPSA 20.2	✓ Ro5	✓ Clean	`C[C@H](c1ccccc1)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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL456414	Q9BPW9	—	358.5 Da LogP 4.67 TPSA 63.6	✓ Ro5	Alert	`C=C1CC[C@@H]2C(C)(C)CCC[C@@]2(C)[C@@H]1CC1=C(O)…`
CHEMBL456619	Q9BPW9	—	344.5 Da LogP 5.75 TPSA 49.7	1 viol.	Alert	`COc1ccc(O)c(O)c1/C=C1\[C@@H](C)CC[C@H]2C(C)(C)C…`
CHEMBL456844	Q9BPW9	—	340.5 Da LogP 5.07 TPSA 35.5	1 viol.	✓ Clean	`CC1=CC[C@H]2C(C)(C)CCC[C@]2(C)[C@H]1/C=C1\C=C2O…`
CHEMBL456845	Q9BPW9	—	384.5 Da LogP 5.58 TPSA 44.8	1 viol.	✓ Clean	`COc1c(C[C@H]2C(C)=CC[C@H]3C(C)(C)CCC[C@]23C)cc2…`
CHEMBL459574	Q9BPW9	—	312.5 Da LogP 4.81 TPSA 34.1	✓ Ro5	Alert	`CC1=CC[C@@H]2C(C)(C)CCC[C@@]2(C)[C@@H]1CC1=CC(=…`
CHEMBL461471	Q9BPW9	—	314.5 Da LogP 5.44 TPSA 40.5	1 viol.	✓ Clean	`C=C1CC[C@@H]2C(C)(C)CCC[C@@]2(C)[C@@H]1Cc1cc(O)…`
CHEMBL514876	Q9BPW9	—	358.5 Da LogP 4.67 TPSA 63.6	✓ Ro5	Alert	`COC1=CC(=O)C(O)=C(/C=C2\[C@@H](C)CC[C@H]3C(C)(C…`
CHEMBL517425	Q9BPW9	—	372.5 Da LogP 4.90 TPSA 52.6	✓ Ro5	Alert	`COC1=CC(=O)C(=O)C(C[C@@]2(C)C3=C(CC[C@@H]2C)C(C…`

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
ZINC3200262	0.842	252.3 Da LogP 2.95 TPSA 51.2	✓ Ro5	Alert	`CC(=O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC36456728	0.800	224.3 Da LogP 3.12 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC1039926	0.625	220.3 Da LogP 3.29 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C#Cc2ccccc2)cc1`
ZINC143028	0.625	228.3 Da LogP 4.04 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(Sc2ccccc2)cc1`
ZINC1440490	0.625	222.3 Da LogP 4.06 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(/C=C/c2ccccc2)cc1`
ZINC14981993	0.625	224.3 Da LogP 3.12 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1cccc(C(=O)c2ccccc2)c1`
ZINC1562037	0.625	210.3 Da LogP 3.48 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(Cc2ccccc2)cc1`
ZINC1675845	0.625	230.3 Da LogP 3.89 TPSA 20.2	✓ Ro5	✓ Clean	`C[C@@H](O)c1ccc(Sc2ccccc2)cc1`
ZINC1675948	0.625	226.3 Da LogP 3.33 TPSA 41.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(NNc2ccccc2)cc1`
ZINC1732765	0.625	246.3 Da LogP -2.20 TPSA 108.7	✓ Ro5	✓ Clean	`O=S(=O)(CCO)CCS(=O)(=O)CCO`
ZINC1845686	0.625	224.3 Da LogP 3.67 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(CCc2ccccc2)cc1`
ZINC2045615	0.625	230.3 Da LogP 3.89 TPSA 20.2	✓ Ro5	✓ Clean	`C[C@H](O)c1ccc(Sc2ccccc2)cc1`
ZINC21999250	0.625	211.3 Da LogP 3.63 TPSA 29.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(Nc2ccccc2)cc1`
ZINC261810	0.625	212.2 Da LogP 3.68 TPSA 26.3	✓ Ro5	✓ Clean	`CC(=O)c1ccc(Oc2ccccc2)cc1`
ZINC35632288	0.625	214.3 Da LogP 3.53 TPSA 29.5	✓ Ro5	✓ Clean	`C[C@H](O)c1ccc(Oc2ccccc2)cc1`
ZINC35632289	0.625	214.3 Da LogP 3.53 TPSA 29.5	✓ Ro5	✓ Clean	`C[C@@H](O)c1ccc(Oc2ccccc2)cc1`
ZINC4798948	0.625	224.3 Da LogP 4.30 TPSA 41.8	✓ Ro5	Alert	`CC(=O)c1ccc(/N=N/c2ccccc2)cc1`
ZINC1765221	0.619	212.3 Da LogP 3.20 TPSA 20.2	✓ Ro5	✓ Clean	`C[C@H](O)C(c1ccccc1)c1ccccc1`
ZINC2032454	0.619	212.3 Da LogP 3.20 TPSA 20.2	✓ Ro5	✓ Clean	`C[C@@H](O)C(c1ccccc1)c1ccccc1`
ZINC50452	0.615	240.3 Da LogP 3.11 TPSA 43.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(OC(=O)c2ccccc2)cc1`
ZINC586797	0.615	239.3 Da LogP 3.14 TPSA 46.2	✓ Ro5	✓ Clean	`CC(=O)c1ccc(NC(=O)c2ccccc2)cc1`
ZINC1672966	0.611	210.2 Da LogP 2.75 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1)c1ccccc1`
ZINC1401590	0.600	244.3 Da LogP 3.06 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc([S@](=O)c2ccccc2)cc1`
ZINC143035	0.600	260.3 Da LogP 2.72 TPSA 51.2	✓ Ro5	✓ Clean	`CC(=O)c1ccc(S(=O)(=O)c2ccccc2)cc1`
ZINC34354396	0.600	224.3 Da LogP 4.04 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc([C@@H](C)c2ccccc2)cc1`
ZINC34354398	0.600	224.3 Da LogP 4.04 TPSA 17.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc([C@H](C)c2ccccc2)cc1`
ZINC4073660	0.600	244.3 Da LogP 3.06 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc([S@@](=O)c2ccccc2)cc1`
ZINC56557	0.600	238.3 Da LogP 3.76 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccc(-c2ccc(C(C)=O)cc2)cc1`
ZINC1720279	0.591	212.3 Da LogP 3.52 TPSA 20.2	✓ Ro5	✓ Clean	`C[C@@H](c1ccccc1)[C@H](O)c1ccccc1`
ZINC1720280	0.591	212.3 Da LogP 3.52 TPSA 20.2	✓ Ro5	✓ Clean	`C[C@H](c1ccccc1)[C@H](O)c1ccccc1`
ZINC1720281	0.591	212.3 Da LogP 3.52 TPSA 20.2	✓ Ro5	✓ Clean	`C[C@@H](c1ccccc1)[C@@H](O)c1ccccc1`
ZINC1720282	0.591	212.3 Da LogP 3.52 TPSA 20.2	✓ Ro5	✓ Clean	`C[C@H](c1ccccc1)[C@@H](O)c1ccccc1`
ZINC141045875	0.583	250.3 Da LogP -0.10 TPSA 63.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCC=O`
ZINC15148066	0.583	222.4 Da LogP 3.78 TPSA 20.2	✓ Ro5	✓ Clean	`C=C1CC[C@H]2C(C)(C)CCC[C@@]2(C)[C@H]1CO`
ZINC336592	0.583	224.3 Da LogP 3.12 TPSA 34.1	✓ Ro5	✓ Clean	`CC(=O)c1ccccc1C(=O)c1ccccc1`
ZINC12359951	0.579	214.3 Da LogP 2.45 TPSA 40.5	✓ Ro5	✓ Clean	`O[C@@H](c1ccccc1)[C@H](O)c1ccccc1`
ZINC12501520	0.579	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1577122	0.579	208.3 Da LogP 4.64 TPSA 0.0	✓ Ro5	✓ Clean	`C/C(=C(/C)c1ccccc1)c1ccccc1`
ZINC1590838	0.579	342.4 Da LogP 3.82 TPSA 68.3	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccccc2)cc1)c1ccccc1`
ZINC16133932	0.579	474.5 Da LogP 4.88 TPSA 102.4	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccc(C(=O)C(=O)c3cccc…`
ZINC1720954	0.579	210.3 Da LogP 4.59 TPSA 0.0	✓ Ro5	✓ Clean	`C[C@@H](c1ccccc1)[C@@H](C)c1ccccc1`
ZINC1720957	0.579	210.3 Da LogP 4.59 TPSA 0.0	✓ Ro5	✓ Clean	`C[C@H](c1ccccc1)[C@H](C)c1ccccc1`
ZINC3123872	0.579	208.3 Da LogP 4.64 TPSA 0.0	✓ Ro5	✓ Clean	`C/C(=C(\C)c1ccccc1)c1ccccc1`
ZINC3874716	0.579	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC388745	0.579	214.3 Da LogP 2.45 TPSA 40.5	✓ Ro5	✓ Clean	`O[C@@H](c1ccccc1)[C@@H](O)c1ccccc1`
ZINC4283769	0.579	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.579	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	0.579	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.579	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC68564262	0.579	210.3 Da LogP 4.59 TPSA 0.0	✓ Ro5	✓ Clean	`C[C@H](c1ccccc1)[C@@H](C)c1ccccc1`

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.