Protein profile

VK055_0618

formate dehydrogenase, beta subunit

Genome: KpATCC43816

Gene: AIK79241.1 fdxH2 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQB9

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Amino acids 294

Annotations 9

Features 30

PDB binders 14

Druggability 0.478

Overview

Basic information about this protein and its source genome.

Accession: VK055_0618
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK79241.1 fdxH2
Status: annotated
Amino acids: 294
Structure source: AlphaFold + ColabFold

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0015944 The chemical reactions and pathways by which formate is converted to CO2. 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:0045333 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration). GO:0009326 An enzyme complex that catalyzes the dehydrogenation of formate to produce carbon dioxide (CO2). GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 (%): 35.632
Localization: CytoplasmicMembrane
ColabFold pLDDT: 96.19

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 0.478

Structure A0A0H3GQB9

Pocket Pocket 1

P2Rank 0.107

Structure A0A0H3GQB9

Pocket Pocket 1

ColabFold model

FPocket 0.503 · Pocket 1

P2Rank 0.128 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 151 / 4744 genomes with a hit

Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0015944 The chemical reactions and pathways by which formate is converted to CO2.
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:0045333 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).
GO:0009326 An enzyme complex that catalyzes the dehydrogenation of formate to produce carbon dioxide (CO2).
GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0036397 Catalysis of the reaction: formate + a quinone = CO2 + a quinol.
GO:0046872 Binding to a metal ion.
GO:0009061 The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which uses compounds other than oxygen (e.g. nitrate, sulfate) as the terminal electron acceptor.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records

Show feature table

Start	End	DB	Term	Name
124	153	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
124	153	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
248	294	FunFam	G3DSA:1.20.5.480:FF:000001	Formate dehydrogenase iron-sulfur subunit
91	123	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
91	123	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
38	50	Pfam	PF12800	4Fe-4S binding domain
38	50	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
7	166	Gene3D	G3DSA:3.30.70.20	-
2	291	PANTHER	PTHR43545	FORMATE DEHYDROGENASE, NITRATE-INDUCIBLE, IRON-SULFUR SUBUNIT
246	289	Pfam	PF09163	Formate dehydrogenase N, transmembrane
246	289	InterPro	IPR015246	Formate dehydrogenase, transmembrane
133	144	ProSitePatterns	PS00198	4Fe-4S ferredoxin-type iron-sulfur binding region signature.
133	144	InterPro	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site
260	277	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
92	188	Pfam	PF13247	4Fe-4S dicluster domain
92	188	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
247	294	Gene3D	G3DSA:1.20.5.480	Single helix bin
247	294	InterPro	IPR038384	Formate dehydrogenase, C-terminal domain superfamily
7	290	NCBIfam	TIGR01582	formate dehydrogenase subunit beta
7	290	InterPro	IPR006470	Formate dehydrogenase iron-sulphur subunit, Proteobacteria
26	262	SUPERFAMILY	SSF54862	4Fe-4S ferredoxins
278	294	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	259	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
30	60	ProSiteProfiles	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
30	60	InterPro	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain
1	294	PIRSF	PIRSF036298	FDH_4Fe4S
1	294	InterPro	IPR014603	Formate dehydrogenase iron-sulphur subunit
32	228	Gene3D	G3DSA:3.30.70.20	-
31	238	CDD	cd10558	FDH-N
31	238	InterPro	IPR006470	Formate dehydrogenase iron-sulphur subunit, Proteobacteria

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_A0A0H3GQB9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_0618	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				0.005
5				0.001
6				0.0
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	3.59	0.107
2	2.94	0.076
3	2.39	0.052
4	2.19	0.043
5	2.01	0.036

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
4				0.006
3				0.002
7				0.002
13				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	3.96	0.128
2	2.95	0.076
3	2.78	0.069
4	2.7	0.065
5	1.95	0.034

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
2MD	1H0H	Q8GC87	742.6 Da LogP -2.53 TPSA 346.6	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…`
3PH	1Q16	P11349	705.0 Da LogP 12.07 TPSA 119.4	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O…`
6MO	1KQF	P0AAJ3	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo+6]`
AGA	1Q16	P11349	455.5 Da LogP 1.85 TPSA 151.7	✓ Ro5	✓ Clean	`CCCCCCCC(=O)O[C@H](COC(=O)CCCC)COP(=O)([O-])OC[…`
BSY	5CHC	G8QM54	128.0 Da LogP -2.25 TPSA 60.4	✓ Ro5	✓ Clean	`O[Se](=O)[O-]`
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	6F0K	D0MDD5	295.8 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]2S[Fe]3[S]2[Fe]1S3`
H2S	6SDV	Q72EJ0	34.1 Da LogP 0.11 TPSA 0.0	✓ Ro5	✓ Clean	`S`
HQO	1KQG	P0AAJ3	259.3 Da LogP 3.69 TPSA 47.2	✓ Ro5	Alert	`CCCCCCCc1cc(c2ccccc2[n+]1[O-])O`
MD1	1Q16	P11349	740.6 Da LogP -2.13 TPSA 358.0	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=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	1R27	P11349	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo]`
PCI	1Y4Z	P11349	266.3 Da LogP 4.66 TPSA 20.2	✓ Ro5	✓ Clean	`c1(c(c(c(c(c1Cl)Cl)Cl)Cl)Cl)O`
W	6SDV	Q72EJ0	183.8 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[W+6]`

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
ZINC1529471	1.000	266.3 Da LogP 4.66 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1c(Cl)c(Cl)c(Cl)c(Cl)c1Cl`
ZINC1529909	1.000	259.3 Da LogP 3.69 TPSA 47.2	✓ Ro5	Alert	`CCCCCCCc1cc(O)c2ccccc2[n+]1[O-]`
ZINC225408	0.900	247.9 Da LogP 3.71 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1c(Cl)c(Cl)c(O)c(Cl)c1Cl`
ZINC154748	0.818	247.9 Da LogP 3.71 TPSA 40.5	✓ Ro5	Alert	`Oc1c(O)c(Cl)c(Cl)c(Cl)c1Cl`
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`
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)(…`
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`
ZINC4521879	0.650	386.5 Da LogP 4.73 TPSA 78.9	✓ Ro5	✓ Clean	`CCCCCC(=O)OCC(COC(=O)CCCCC)OC(=O)CCCCC`
ZINC137999083	0.622	424.5 Da LogP 4.87 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCC(=O)OC[C@H](O)COP(=O)(O)O`
ZINC42851452	0.622	424.5 Da LogP 4.87 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC62624856	0.622	382.4 Da LogP 3.70 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)COP(=O)(O)O`
ZINC62624861	0.622	382.4 Da LogP 3.70 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC8218993	0.622	410.5 Da LogP 4.48 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)COP(=O)(O)O`
ZINC8219000	0.622	410.5 Da LogP 4.48 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC102190506	0.620	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCCN)OC(=O)CC…`
ZINC102190512	0.620	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)C…`
ZINC12501413	0.610	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC12958448	0.610	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC1532555	0.610	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC16546189	0.610	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC2159505	0.610	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3073318	0.610	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869963	0.610	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869965	0.610	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC9334496	0.610	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC13552119	0.600	270.2 Da LogP 0.58 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC27416437	0.600	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCCN)OC(=O)CCCCC`
ZINC33902364	0.600	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)CCC…`
ZINC36079847	0.591	344.5 Da LogP 4.15 TPSA 72.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO)OC(=O)CCCCCCC`
ZINC8214428	0.591	344.5 Da LogP 4.15 TPSA 72.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO)OC(=O)CCCCCCC`
ZINC13543394	0.588	455.4 Da LogP 2.15 TPSA 171.7	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](N)C(=O)…`
ZINC4521911	0.585	344.4 Da LogP 3.56 TPSA 78.9	✓ Ro5	✓ Clean	`CCCCC(=O)OCC(COC(=O)CCCC)OC(=O)CCCC`
ZINC85603366	0.585	344.5 Da LogP 4.15 TPSA 72.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OCC(O)COC(=O)CCCCCCC`
ZINC13544781	0.585	482.6 Da LogP 4.22 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@@H](CO[P@](=O)(O)OCC[N+](C)(C)C…`
ZINC13544783	0.585	482.6 Da LogP 4.22 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)…`
ZINC102191158	0.571	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[C@…`
ZINC14880758	0.571	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OC[…`
ZINC62592203	0.571	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC[C…`
ZINC62592204	0.571	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC…`
ZINC96094841	0.571	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC[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.