Protein profile

KP13_02585

Electron transport protein hydN

Genome: KpKP13

Gene: hydN AHE43046.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H1W9

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Amino acids 175

Annotations 2

Features 15

PDB binders 11

Druggability 0.451

Overview

Basic information about this protein and its source genome.

Accession: KP13_02585
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: hydN AHE43046.1
Status: annotated
Amino acids: 175
Structure source: AlphaFold + ColabFold

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. GO:0046872 Binding to a metal ion.

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: Cytoplasmic
ColabFold pLDDT: 94.17

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 0.451

Structure A0A0H3H1W9

Pocket Pocket 2

P2Rank 0.253

Structure A0A0H3H1W9

Pocket Pocket 1

ColabFold model

FPocket 0.302 · Pocket 6

P2Rank 0.22 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 98 / 4744 genomes with a hit

Normalized 0.021

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

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.
GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
89	100	ProSitePatterns	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.
89	100	InterPro	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site
1	170	SUPERFAMILY	SSF54862	4Fe-4S ferredoxins
5	167	Gene3D	G3DSA:3.30.70.20	-
2	22	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
2	22	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
80	109	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
80	109	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
1	171	PANTHER	PTHR42859	OXIDOREDUCTASE
64	130	Gene3D	G3DSA:3.30.70.20	-
55	104	Pfam	PF13247	4Fe-4S dicluster domain
55	104	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
4	155	CDD	cd10554	HycB_like
131	151	Pfam	PF12798	4Fe-4S binding domain
131	151	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain

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_A0A0H3H1W9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02585	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
2				0.451
3				0.409

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	3.37	0.12
2	2.94	0.095
3	2.09	0.047
4	1.32	0.015
5	0.85	0.003

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
6				0.302

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	3.6	0.134
2	2.16	0.051
3	2.08	0.047
4	1.85	0.036

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
6MO	1KQF	P0AAJ3	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo+6]`
CDL	1KQF	P0AAJ3	1464.1 Da LogP 23.31 TPSA 242.6	3 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…`
F3S	6BTM	A5FJF2	295.8 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]2S[Fe]3[S]2[Fe]1S3`
HQO	1KQG	P0AAJ3	259.3 Da LogP 3.69 TPSA 47.2	✓ Ro5	Alert	`CCCCCCCc1cc(c2ccccc2[n+]1[O-])O`
MGD	1KQF	P0AAJ3	740.6 Da LogP -2.06 TPSA 346.6	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…`
MO	6CZ8	Q7WTT9	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo]`
O	6CZ8	Q7WTT9	18.0 Da LogP -0.82 TPSA 31.5	✓ Ro5	✓ Clean	`O`
PG5	6CZ8	Q7WTT9	178.2 Da LogP 0.31 TPSA 36.9	✓ Ro5	✓ Clean	`COCCOCCOCCOC`
PTE	6X1O	I6U881	1024.8 Da LogP 0.35 TPSA 361.4	3 viol.	✓ Clean	`C1[C@@H]2C3=C([C@H]4[C@@H](O2)NC5=C(N4)C(=O)NC(…`
TAU	6X6U	I6U881	125.1 Da LogP -1.17 TPSA 80.4	✓ Ro5	✓ Clean	`C(CS(=O)(=O)O)N`
UKM	6X1O	I6U881	154.2 Da LogP -0.01 TPSA 74.6	✓ Ro5	✓ Clean	`CCC[C@H](O)S(=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
ZINC1529909	1.000	259.3 Da LogP 3.69 TPSA 47.2	✓ Ro5	Alert	`CCCCCCCc1cc(O)c2ccccc2[n+]1[O-]`
ZINC1692489	1.000	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC4530388	1.000	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5701172	1.000	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC5997861	1.000	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC34764844	0.733	206.3 Da LogP 1.09 TPSA 36.9	✓ Ro5	✓ Clean	`CCCOCCOCCOCCOC`
ZINC102191119	0.708	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@@H](O)CO…`
ZINC58649551	0.708	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](O)CO)…`
ZINC36178999	0.705	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC36179002	0.705	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC140264883	0.688	223.3 Da LogP -0.43 TPSA 72.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCON`
ZINC143705779	0.688	443.5 Da LogP -0.34 TPSA 118.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCON`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC33358855	0.688	207.3 Da LogP -0.36 TPSA 62.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCN`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44583772	0.688	356.5 Da LogP 0.66 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCS`
ZINC5024003	0.688	251.3 Da LogP -0.34 TPSA 72.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCN`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC575432090	0.688	355.4 Da LogP -0.38 TPSA 99.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCON`
ZINC575432265	0.688	399.5 Da LogP -0.36 TPSA 109.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCON`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC71254558	0.688	444.6 Da LogP 0.70 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC71254563	0.688	488.6 Da LogP 0.71 TPSA 92.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC80685077	0.688	427.5 Da LogP -0.28 TPSA 109.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCN`
ZINC83253927	0.688	400.5 Da LogP 0.68 TPSA 73.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC83253930	0.688	224.3 Da LogP 0.61 TPSA 36.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCS`
ZINC83253936	0.688	383.5 Da LogP -0.29 TPSA 99.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCN`
ZINC90556279	0.688	295.4 Da LogP -0.33 TPSA 81.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCN`
ZINC90556280	0.688	339.4 Da LogP -0.31 TPSA 90.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCN`
ZINC90556286	0.688	312.4 Da LogP 0.65 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCS`
ZINC90556287	0.688	268.4 Da LogP 0.63 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCS`
ZINC96503353	0.688	471.6 Da LogP -0.26 TPSA 118.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCN`
ZINC104869865	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…`
ZINC12504289	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC34541308	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC35000839	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC4284463	0.684	250.2 Da LogP -1.82 TPSA 149.2	✓ Ro5	✓ Clean	`O=S(=O)(O)[C@H](O)CC[C@@H](O)S(=O)(=O)O`
ZINC4284464	0.684	250.2 Da LogP -1.82 TPSA 149.2	✓ Ro5	✓ Clean	`O=S(=O)(O)[C@H](O)CC[C@H](O)S(=O)(=O)O`
ZINC4284466	0.684	250.2 Da LogP -1.82 TPSA 149.2	✓ Ro5	✓ Clean	`O=S(=O)(O)[C@@H](O)CC[C@H](O)S(=O)(=O)O`
ZINC45284491	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC80639694	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC8215481	0.684	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC5820131	0.682	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC5820134	0.682	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC104256315	0.667	266.4 Da LogP 3.11 TPSA 74.6	✓ Ro5	✓ Clean	`CCCCCCCCCCC[C@@H](O)S(=O)(=O)O`
ZINC59681871	0.667	322.5 Da LogP 4.67 TPSA 74.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC[C@@H](O)S(=O)(=O)O`
ZINC59681874	0.667	322.5 Da LogP 4.67 TPSA 74.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC[C@H](O)S(=O)(=O)O`

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.