Protein profile

KP13_04904

NADH dehydrogenase

Genome: KpKP13

Gene: AHE45264.1 ndh Structure source: AlphaFold + ColabFold UniProt A0A0H3GMU6

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Amino acids 434

Annotations 3

Features 16

PDB binders 5

Druggability 0.818

Overview

Basic information about this protein and its source genome.

Accession: KP13_04904
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45264.1 ndh
Status: annotated
Amino acids: 434
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:0003955 Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a quinol. GO:0019646 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to oxygen to generate a transmembrane electrochemical gradient.

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: 86.86

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 0.818

Structure A0A0H3GMU6

Pocket Pocket 26

P2Rank 0.944

Structure A0A0H3GMU6

Pocket Pocket 1

ColabFold model

FPocket 0.959 · Pocket 33

P2Rank 0.988 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 155 / 4744 genomes with a hit

Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 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:0003955 Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a quinol.
GO:0019646 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to oxygen to generate a transmembrane electrochemical gradient.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
5	413	Gene3D	G3DSA:3.50.50.100	-
6	338	Pfam	PF07992	Pyridine nucleotide-disulphide oxidoreductase
6	338	InterPro	IPR023753	FAD/NAD(P)-binding domain
168	352	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
168	352	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
6	403	PANTHER	PTHR42913	APOPTOSIS-INDUCING FACTOR 1
6	224	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
6	224	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
172	197	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
310	317	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
7	29	PRINTS	PR00411	Pyridine nucleotide disulphide reductase class-I signature
5	413	FunFam	G3DSA:3.50.50.100:FF:000001	NADH dehydrogenase
115	133	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
8	27	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
172	190	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature
295	317	PRINTS	PR00368	FAD-dependent pyridine nucleotide reductase signature

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_A0A0H3GMU6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04904	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
26				0.818

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	15.37	0.752
2	14.82	0.735
3	6.8	0.348
4	6.68	0.339
5	2.42	0.065

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
33				0.959

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	16.46	0.779
2	12.33	0.647
3	11.71	0.622
4	7.91	0.42
5	1.95	0.041

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.

61 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
4W0	5JWC	Q8I302	427.4 Da LogP 6.13 TPSA 42.1	1 viol.	✓ Clean	`CC1=C(Nc2cccc(c2C1=O)F)c3ccc(cc3)Cc4ccc(cc4)OC(…`
CXS	5JWB	Q8I302	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCCS(=O)(=O)O`
HQO	6BDO	F5L3B8	259.3 Da LogP 3.69 TPSA 47.2	✓ Ro5	Alert	`CCCCCCCc1cc(c2ccccc2[n+]1[O-])O`
MLI	5NA1	Q2FZV7	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
TRT	5JWA	Q8I302	352.5 Da LogP 4.46 TPSA 36.9	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(cc1)OCCOCCOCCOC`

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
CHEMBL5186518	P95160	7.92	412.5 Da LogP 3.78 TPSA 42.0	✓ Ro5	✓ Clean	`CC(C)[C@H]1CO[C@]23CCN(Cc4ccc(OC(F)(F)F)cc4)C[C…`
CHEMBL5201484	P95160	7.92	396.5 Da LogP 3.90 TPSA 32.8	✓ Ro5	✓ Clean	`CC(C)[C@H]1CO[C@]23CCN(Cc4ccc(C(F)(F)F)cc4)C[C@…`
CHEMBL5171834	P95160	7.55	362.9 Da LogP 3.54 TPSA 32.8	✓ Ro5	✓ Clean	`CC(C)[C@H]1CO[C@]23CCN(Cc4ccc(Cl)cc4)C[C@H]2CCC…`
CHEMBL5202255	P95160	7.50	397.4 Da LogP 3.30 TPSA 45.7	✓ Ro5	✓ Clean	`CC(C)[C@H]1CO[C@]23CCN(Cc4ccc(C(F)(F)F)nc4)C[C@…`
CHEMBL5206556	P95160	6.70	358.5 Da LogP 2.89 TPSA 42.0	✓ Ro5	✓ Clean	`COc1ccc(CN2CC[C@]34OC[C@H](C(C)C)N3C(=O)CC[C@@H…`
CHEMBL5182198	P95160	6.47	328.5 Da LogP 2.88 TPSA 32.8	✓ Ro5	✓ Clean	`CC(C)[C@H]1CO[C@]23CCN(Cc4ccccc4)C[C@H]2CCC(=O)…`

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
ZINC1529909	1.000	259.3 Da LogP 3.69 TPSA 47.2	✓ Ro5	Alert	`CCCCCCCc1cc(O)c2ccccc2[n+]1[O-]`
ZINC2004372	1.000	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.926	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC1710230	0.786	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC2030966	0.750	294.4 Da LogP 3.79 TPSA 38.7	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCCO)cc1`
ZINC1592053	0.711	321.5 Da LogP 4.36 TPSA 21.7	✓ Ro5	✓ Clean	`CN(C)CCOCCOc1ccc(C(C)(C)CC(C)(C)C)cc1`
ZINC167273021	0.692	308.4 Da LogP 3.88 TPSA 55.8	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCC(=O)O)cc1`
ZINC25756964	0.645	402.5 Da LogP 1.80 TPSA 73.8	✓ Ro5	✓ Clean	`COCCOCCOCCOc1ccc(OCCOCCOCCOC)cc1`
ZINC1532311	0.639	250.4 Da LogP 3.77 TPSA 29.5	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCO)cc1`
ZINC1857731210	0.631	368.4 Da LogP 3.26 TPSA 32.8	✓ Ro5	✓ Clean	`CC(C)[C@@H]1CO[C@@]23CCN(Cc4ccc(C(F)(F)F)cc4)[C…`
ZINC5188799	0.630	280.5 Da LogP 4.39 TPSA 24.1	✓ Ro5	✓ Clean	`C(CCCNC1CCCCC1)CCNC1CCCCC1`
ZINC4353076	0.628	352.5 Da LogP 4.42 TPSA 68.3	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCCSC(=N)N)cc1`
ZINC1688152	0.622	380.5 Da LogP 3.96 TPSA 55.8	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCC[N+](C)(C)CC(=O)O)c…`
ZINC35650209	0.605	278.4 Da LogP 4.55 TPSA 29.5	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCCCO)cc1`
ZINC226069334	0.605	366.6 Da LogP 3.86 TPSA 38.7	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOC[C@@H](O)C[N+](C)(C)…`
ZINC226069348	0.605	366.6 Da LogP 3.86 TPSA 38.7	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOC[C@H](O)C[N+](C)(C)C…`
ZINC32011214	0.600	363.5 Da LogP 4.13 TPSA 30.9	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCOCCN2CCOCC2)cc1`
ZINC685938638	0.600	253.3 Da LogP 3.64 TPSA 32.9	✓ Ro5	✓ Clean	`Cc1c(-c2ccccc2)[nH]c2cccc(F)c2c1=O`
ZINC1693494	0.588	220.4 Da LogP 4.41 TPSA 9.2	✓ Ro5	✓ Clean	`COc1ccc(C(C)(C)CC(C)(C)C)cc1`
ZINC220528199	0.588	478.6 Da LogP 3.47 TPSA 73.8	✓ Ro5	✓ Clean	`COCCOCCOCCOc1ccc(-c2ccc(OCCOCCOCCOC)cc2)cc1`
ZINC2984023	0.583	344.5 Da LogP 4.47 TPSA 36.9	✓ Ro5	✓ Clean	`COc1ccc(OCCOCCOc2ccc(C(C)(C)C)cc2)cc1`
ZINC34211424	0.571	319.2 Da LogP 2.51 TPSA 36.9	✓ Ro5	✓ Clean	`COCCOCCOCCOc1ccc(Br)cc1`
ZINC95982959	0.571	240.3 Da LogP 2.13 TPSA 36.9	✓ Ro5	✓ Clean	`CCOc1ccc(OCCOCCOC)cc1`
ZINC64844	0.564	264.4 Da LogP 3.86 TPSA 46.5	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCC(=O)O)cc1`
ZINC126169091	0.556	256.3 Da LogP 1.45 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOc1ccc(O)cc1`
ZINC14630111	0.556	211.3 Da LogP 1.31 TPSA 53.7	✓ Ro5	Alert	`COCCOCCOc1ccc(N)cc1`
ZINC90556265	0.556	255.3 Da LogP 1.33 TPSA 62.9	✓ Ro5	Alert	`COCCOCCOCCOc1ccc(N)cc1`
ZINC226069639	0.553	365.6 Da LogP 4.15 TPSA 50.7	✓ Ro5	✓ Clean	`CC(C)NC[C@@H](O)COCCOc1ccc(C(C)(C)CC(C)(C)C)cc1`
ZINC226069650	0.553	365.6 Da LogP 4.15 TPSA 50.7	✓ Ro5	✓ Clean	`CC(C)NC[C@H](O)COCCOc1ccc(C(C)(C)CC(C)(C)C)cc1`
ZINC142979416	0.553	284.3 Da LogP 1.44 TPSA 74.2	✓ Ro5	✓ Clean	`COCCOCCOCCOc1ccc(C(=O)O)cc1`
ZINC4775495	0.553	246.4 Da LogP 4.97 TPSA 9.2	✓ Ro5	✓ Clean	`C=CCOc1ccc(C(C)(C)CC(C)(C)C)cc1`
ZINC1857713799	0.549	396.4 Da LogP 2.83 TPSA 49.9	✓ Ro5	✓ Clean	`CC(C)[C@@H]1CO[C@@]23CCN(C(=O)Cc4ccc(C(F)(F)F)c…`
ZINC1698725	0.541	314.4 Da LogP 4.46 TPSA 27.7	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc(OCCOCCOc2ccccc2)cc1`
ZINC1857731857	0.539	383.4 Da LogP 2.30 TPSA 62.7	✓ Ro5	✓ Clean	`CC(C)[C@@H]1CO[C@@]23CCN(C(=O)c4ccc(C(F)(F)F)nc…`
ZINC1857722404	0.537	362.9 Da LogP 2.47 TPSA 49.9	✓ Ro5	✓ Clean	`CC(C)[C@@H]1CO[C@@]23CCN(C(=O)Cc4ccc(Cl)cc4)[C@…`
ZINC4200484	0.537	262.4 Da LogP 4.18 TPSA 21.8	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OC[C@@H]2CO2)cc1`
ZINC4200485	0.537	262.4 Da LogP 4.18 TPSA 21.8	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OC[C@H]2CO2)cc1`
ZINC16889914	0.535	308.5 Da LogP 4.41 TPSA 59.1	✓ Ro5	✓ Clean	`CC(C)(C)CC(C)(C)c1ccc(OCCSC(=N)N)cc1`
ZINC2509149	0.531	211.4 Da LogP 4.27 TPSA 12.0	✓ Ro5	✓ Clean	`CCCCCCCCNC1CCCCC1`
ZINC130127586	0.529	260.4 Da LogP 1.38 TPSA 58.2	✓ Ro5	✓ Clean	`O=S(=O)(NCCNC1CCCCCC1)C1CC1`
ZINC1857724257	0.529	356.5 Da LogP 3.54 TPSA 32.8	✓ Ro5	✓ Clean	`CC(C)[C@@H]1CO[C@@]23CCN(Cc4ccc(C(C)(C)C)cc4)[C…`
ZINC1857717617	0.526	384.4 Da LogP 3.14 TPSA 42.0	✓ Ro5	✓ Clean	`CC(C)[C@@H]1CO[C@@]23CCN(Cc4cccc(OC(F)(F)F)c4)[…`
ZINC70027652	0.526	226.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`COCCOCCOc1ccc(CO)cc1`
ZINC126188107	0.525	319.4 Da LogP 0.39 TPSA 97.1	✓ Ro5	✓ Clean	`COCCOCCOCCOc1ccc(S(N)(=O)=O)cc1`
ZINC1857726557	0.522	376.9 Da LogP 2.86 TPSA 49.9	✓ Ro5	✓ Clean	`CC(C)[C@@H]1CO[C@@]23CCN(C(=O)CCc4ccc(Cl)cc4)[C…`
ZINC1857734870	0.522	352.8 Da LogP 3.04 TPSA 32.8	✓ Ro5	✓ Clean	`CC(C)[C@@H]1CO[C@@]23CCN(Cc4ccc(F)c(Cl)c4)[C@@H…`
ZINC19367005	0.519	224.4 Da LogP 2.83 TPSA 24.1	✓ Ro5	✓ Clean	`C1CCC(NCCNC2CCCCC2)CC1`
ZINC19432075	0.514	231.1 Da LogP 2.47 TPSA 18.5	✓ Ro5	✓ Clean	`COCCOc1ccc(Br)cc1`
ZINC42226887	0.514	278.1 Da LogP 2.32 TPSA 18.5	✓ Ro5	✓ Clean	`COCCOc1ccc(I)cc1`
ZINC1600788	0.514	234.4 Da LogP 4.55 TPSA 9.2	✓ Ro5	✓ Clean	`COCc1ccc(C(C)(C)CC(C)(C)C)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.