Protein profile

KP13_02576

Formate hydrogenlyase subunit 5

Genome: KpKP13

Gene: AHE43037.1 hycE Structure source: AlphaFold + ColabFold UniProt A0A0H3H1X8
Amino acids 569
Annotations 6
Features 21
PDB binders 29
Druggability 0.827

Overview

Basic information about this protein and its source genome.

Accession
KP13_02576
Gene
AHE43037.1 hycE
Status
annotated
Amino acids
569
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
29.851
Human E-value
8.11e-09
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
91.98

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 0.827
Structure A0A0H3H1X8
Pocket Pocket 3
P2Rank 0.887
Structure A0A0H3H1X8
Pocket Pocket 1
ColabFold model
FPocket 0.901 · Pocket 3
P2Rank 0.602 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 528 / 4744 genomes with a hit
Normalized 0.111

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0016151 Binding to a nickel (Ni) cation.
  • GO:0008137 Catalysis of the reaction: NADH + ubiquinone + 5 H+(in) = NAD+ + ubiquinol + 4 H+(out).
  • GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
  • GO:0016651 Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
  • GO:0048038 Binding to a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
296 464 Pfam PF00346 Respiratory-chain NADH dehydrogenase, 49 Kd subunit
296 464 InterPro IPR001135 NADH-quinone oxidoreductase, subunit D
466 537 Pfam PF00346 Respiratory-chain NADH dehydrogenase, 49 Kd subunit
466 537 InterPro IPR001135 NADH-quinone oxidoreductase, subunit D
36 152 Pfam PF00329 Respiratory-chain NADH dehydrogenase, 30 Kd subunit
36 152 InterPro IPR001268 NADH:ubiquinone oxidoreductase, 30kDa subunit
218 286 Pfam PF00374 Nickel-dependent hydrogenase
218 286 InterPro IPR001501 Nickel-dependent hydrogenase, large subunit
180 537 FunFam G3DSA:1.10.645.10:FF:000004 Hydrogenase 3, large subunit
193 537 SUPERFAMILY SSF56762 HydB/Nqo4-like
193 537 InterPro IPR029014 [NiFe]-hydrogenase, large subunit
2 134 FunFam G3DSA:3.30.460.80:FF:000003 Formate hydrogenlyase subunit 5
2 134 Gene3D G3DSA:3.30.460.80 NADH:ubiquinone oxidoreductase, 30kDa subunit
2 134 InterPro IPR037232 NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily
14 546 PANTHER PTHR43485 HYDROGENASE-4 COMPONENT G
180 537 Gene3D G3DSA:1.10.645.10 -
180 537 InterPro IPR029014 [NiFe]-hydrogenase, large subunit
9 194 SUPERFAMILY SSF143243 Nqo5-like
9 194 InterPro IPR037232 NADH:ubiquinone oxidoreductase, 30kDa subunit superfamily
216 227 ProSitePatterns PS00535 Respiratory chain NADH dehydrogenase 49 Kd subunit signature.
216 227 InterPro IPR014029 NADH:ubiquinone oxidoreductase, 49kDa subunit, conserved site

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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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_A0A0H3H1X8
AlphaFold full sequence Viewing
ColabFold KP13_02576
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
3 0.827

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 20.18 0.851
2 12.82 0.663
3 8.95 0.479
4 4.43 0.187
5 2.83 0.088

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.

79 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
3PE F2Z626 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
BCR Q8DJD9 536.9 Da LogP 12.61 TPSA 0.0 2 viol. ✓ Clean CC1=C(C(CCC1)(C)C)\C=C\C(=C\C=C\C(=C\C=C\C=C(/C…
CDL W5PJ73 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
CPL F2Z626 758.1 Da LogP 10.94 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])OC…
DCQ Q56220 322.4 Da LogP 4.49 TPSA 52.6 ✓ Ro5 Alert CCCCCCCCCCC1=C(C(=O)C(=C(C1=O)OC)OC)C
DGD Q8DJD9 949.3 Da LogP 7.61 TPSA 231.1 4 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[C@H]1[C@@H]([C…
EHZ F2Z626 584.7 Da LogP 3.04 TPSA 182.5 2 viol. ✓ Clean CCCCCCCCCCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H]…
FES Q8DJD9 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
HQH Q56220 415.6 Da LogP 5.05 TPSA 71.6 1 viol. ✓ Clean C/C=C(\C)/[C@@H]([C@H](C)/C=C(\C)/C=C/C/C(=C/CC…
HQK Q56220 364.9 Da LogP 5.24 TPSA 34.9 1 viol. ✓ Clean CC(C)(C)c1ccc(cc1)CSC2=C(C(=O)N(N=C2)C(C)(C)C)Cl
HQW Q56220 397.4 Da LogP 4.66 TPSA 91.8 ✓ Ro5 ✓ Clean CC1=C(OC(=C(C1=O)C)OC)[C@H]2C/C(=C/C(=C/c3ccc(c…
LHG Q8DJD9 723.0 Da LogP 9.89 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@…
LMG Q8DJD9 787.2 Da LogP 9.78 TPSA 152.0 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[C@H]1[C@@H]([C…
LMN F2Z626 1005.2 Da LogP -1.68 TPSA 357.1 3 viol. ✓ Clean CCCCCCCCCCC(CCCCCCCCCC)(CO[C@@H]1[C@@H]([C@@H](…
LMT F2Z626 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…
NFU Q8U0Z6 195.6 Da LogP -0.25 TPSA 64.7 ✓ Ro5 ✓ Clean C(=O)[Fe](C#N)(C#N)[Ni]
PC1 W5PJ73 790.2 Da LogP 12.17 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])…
PGT Q8DJD9 751.0 Da LogP 10.67 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)O[C@@H](COC(=O)CCCCCCCCCC…
PL9 Q8DJD9 749.2 Da LogP 16.57 TPSA 34.1 2 viol. Alert CC1=C(C(=O)C(=CC1=O)CC=C(C)CCC=C(C)CCC=C(C)CCC=…
PLC F2Z626 622.8 Da LogP 8.12 TPSA 108.4 2 viol. ✓ Clean CCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)…
PNS W5PJ73 358.4 Da LogP -0.96 TPSA 145.2 1 viol. ✓ Clean CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
PQN Q8DJD9 450.7 Da LogP 9.16 TPSA 34.1 1 viol. Alert CC1=C(C(=O)c2ccccc2C1=O)C\C=C(/C)\CCC[C@H](C)CC…
PSC F2Z626 759.1 Da LogP 11.58 TPSA 108.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC[N…
SMA Q56220 514.7 Da LogP 6.14 TPSA 87.4 2 viol. ✓ Clean C/C=C(\C)/C=C/C=C[C@@H]([C@@H](C)[C@H]([C@@H](C…
SQD Q8DJD9 795.1 Da LogP 8.12 TPSA 186.1 3 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](COC1[C@@H]([C@H]([C…
T7X F2Z626 887.1 Da LogP 9.17 TPSA 209.5 4 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OC1[C@@…
UQ1 Q56220 250.3 Da LogP 2.32 TPSA 52.6 ✓ Ro5 Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)CC=C(C)C
UQ9 F2Z626 795.2 Da LogP 16.13 TPSA 52.6 2 viol. Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CC\C=C(/C)…
ZMP F2Z626 568.7 Da LogP 4.07 TPSA 162.3 1 viol. ✓ Clean CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(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.