Protein profile

KP13_05320

Formate dehydrogenase H

Genome: KpKP13

Gene: AHE44162.1 fdhF Structure source: AlphaFold + ColabFold UniProt A0A0H3GR17

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Amino acids 736

Annotations 10

Features 38

PDB binders 10

Druggability 1

Overview

Basic information about this protein and its source genome.

Accession: KP13_05320
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44162.1 fdhF
Status: annotated
Amino acids: 736
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:0015942 The chemical reactions and pathways involving formate, also known as methanoate, the anion HCOO- derived from methanoic (formic) acid. GO:0008863 Catalysis of the reaction: formate + NAD+ = CO2 + NADH. GO:0043546 Binding to a molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:1990204 Any protein complex that possesses oxidoreductase activity.

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: 96.14

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 1

Structure A0A0H3GR17

Pocket Pocket 1

P2Rank 0.988

Structure A0A0H3GR17

Pocket Pocket 1

ColabFold model

FPocket 1 · Pocket 1

P2Rank 0.984 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 558 / 4744 genomes with a hit

Normalized 0.118

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 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:0015942 The chemical reactions and pathways involving formate, also known as methanoate, the anion HCOO- derived from methanoic (formic) acid.
GO:0008863 Catalysis of the reaction: formate + NAD+ = CO2 + NADH.
GO:0043546 Binding to a molybdopterin cofactor (Moco), essential for the catalytic activity of some enzymes, e.g. sulfite oxidase, xanthine dehydrogenase, and aldehyde oxidase. The cofactor consists of a mononuclear molybdenum (Mo-molybdopterin) or tungsten ion (W-molybdopterin) coordinated by one or two molybdopterin ligands.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:1990204 Any protein complex that possesses oxidoreductase activity.
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.
GO:0003954 Catalysis of the reaction: NADH + H+ + acceptor = NAD+ + reduced acceptor.
GO:0022904 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.

Sequence Features

Domain/signature hits from InterPro and related databases.

38 records

Show feature table

Start	End	DB	Term	Name
81	508	Pfam	PF00384	Molybdopterin oxidoreductase
81	508	InterPro	IPR006656	Molybdopterin oxidoreductase
160	354	FunFam	G3DSA:3.40.228.10:FF:000002	Formate dehydrogenase subunit alpha
555	713	PIRSF	PIRSF000144	CbbBc
72	459	PIRSF	PIRSF000144	CbbBc
455	472	ProSitePatterns	PS00490	Prokaryotic molybdopterin oxidoreductases signature 2.
455	472	InterPro	IPR006655	Molybdopterin oxidoreductase, prokaryotic, conserved site
6	16	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
27	706	NCBIfam	TIGR01591	formate dehydrogenase subunit alpha
27	706	InterPro	IPR006478	Formate dehydrogenase, alpha subunit
593	709	Gene3D	G3DSA:2.40.40.20	-
592	708	CDD	cd02790	MopB_CT_Formate-Dh_H
592	708	InterPro	IPR041925	Formate dehydrogenase H, molybdopterin-binding domain
21	584	SUPERFAMILY	SSF53706	Formate dehydrogenase/DMSO reductase, domains 1-3
21	75	Gene3D	G3DSA:2.20.25.90	-
160	354	Gene3D	G3DSA:3.40.228.10	Dimethylsulfoxide Reductase, domain 2
1	5	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
596	703	Pfam	PF01568	Molydopterin dinucleotide binding domain
596	703	InterPro	IPR006657	Molybdopterin dinucleotide-binding domain
22	736	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
21	74	SMART	SM00926	Molybdop_Fe4S4_2
21	74	InterPro	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain
17	21	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
93	552	Gene3D	G3DSA:3.40.50.740	-
21	76	ProSiteProfiles	PS51669	Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
21	76	InterPro	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain
1	21	Phobius	SIGNAL_PEPTIDE	Signal peptide region
636	663	ProSitePatterns	PS00932	Prokaryotic molybdopterin oxidoreductases signature 3.
636	663	InterPro	IPR006655	Molybdopterin oxidoreductase, prokaryotic, conserved site
26	585	CDD	cd02753	MopB_Formate-Dh-H
26	585	InterPro	IPR041924	Formate dehydrogenase H, N-terminal
22	709	PANTHER	PTHR43105	RESPIRATORY NITRATE REDUCTASE
21	73	Pfam	PF04879	Molybdopterin oxidoreductase Fe4S4 domain
21	73	InterPro	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain
586	720	SUPERFAMILY	SSF50692	ADC-like
586	720	InterPro	IPR009010	Aspartate decarboxylase-like domain superfamily
21	75	FunFam	G3DSA:2.20.25.90:FF:000001	Formate dehydrogenase subunit alpha
1	26	SignalP_EUK	SignalP-noTM	SignalP-noTM

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_A0A0H3GR17	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05320	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
1				1.0

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	35.53	0.953
2	4.46	0.189
3	3.5	0.128
4	1.83	0.035
5	1.68	0.029

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				1.0
15				0.309

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	22.67	0.882
2	13.3	0.681
3	3.76	0.144
4	1.86	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.

60 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	2IV2	P07658	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@@](=…`
4MO	1AA6	P07658	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo+4]`
6MO	6TG9	D5AQH0	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo+6]`
FES	6TG9	D5AQH0	175.8 Da LogP 1.29 TPSA 0.0	✓ Ro5	✓ Clean	`S1[Fe]S[Fe]1`
H2S	6TG9	D5AQH0	34.1 Da LogP 0.11 TPSA 0.0	✓ Ro5	✓ Clean	`S`
LCP	2V3V	P81186	99.4 Da LogP -4.76 TPSA 92.2	✓ Ro5	✓ Clean	`[O-]Cl(=O)(=O)=O`
MGD	2JIM	P81186	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	2JIM	P81186	95.9 Da LogP -0.00 TPSA 0.0	✓ Ro5	✓ Clean	`[Mo]`
MOS	3ML1	P39185	161.0 Da LogP 0.14 TPSA 34.1	✓ Ro5	✓ Clean	`O=[Mo](=O)S`
NO2	1FDI	P07658	46.0 Da LogP 0.25 TPSA 52.5	✓ Ro5	✓ Clean	`N(=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
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)(…`
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)[…`
ZINC100058967	0.568	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@H]3O[C@H](CO[P@](=O)(O)OP(=O)…`
ZINC12504287	0.568	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(…`
ZINC12504288	0.568	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@H]3O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC31308647	0.568	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc(=O)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(…`
ZINC71774763	0.547	432.3 Da LogP -2.23 TPSA 198.3	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@](=O)(O)N3CCOCC3…`
ZINC106686432	0.543	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP…`
ZINC12958393	0.543	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CO[P@](=O)(O)O…`
ZINC35024781	0.543	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)O…`
ZINC35024785	0.543	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)O…`
ZINC35024786	0.543	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)…`
ZINC4261903	0.543	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)O…`
ZINC80601236	0.543	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)O…`
ZINC95921560	0.543	428.2 Da LogP -2.03 TPSA 226.5	2 viol.	✓ Clean	`O=c1[nH]cnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)O…`
ZINC12503703	0.536	427.2 Da LogP -1.42 TPSA 232.3	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(…`
ZINC8215878	0.536	427.2 Da LogP -1.42 TPSA 232.3	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O…`
ZINC17375772	0.530	459.3 Da LogP -1.46 TPSA 232.6	2 viol.	✓ Clean	`Nc1nc(S)c2ncn([C@@H]3O[C@@H](CO[P@](=O)(O)OP(=O…`
ZINC8618621	0.530	459.3 Da LogP -1.46 TPSA 232.6	2 viol.	✓ Clean	`Nc1nc(S)c2ncn([C@H]3O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8618622	0.530	459.3 Da LogP -1.46 TPSA 232.6	2 viol.	✓ Clean	`Nc1nc(S)c2ncn([C@@H]3O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8618623	0.530	459.3 Da LogP -1.46 TPSA 232.6	2 viol.	✓ Clean	`Nc1nc(S)c2ncn([C@H]3O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC4743771	0.524	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC4743772	0.524	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC4743774	0.524	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc…`
ZINC4743775	0.524	361.3 Da LogP -2.70 TPSA 182.6	1 viol.	✓ Clean	`CS(=O)(=O)OC[C@@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)n…`
ZINC100727895	0.500	347.2 Da LogP -2.50 TPSA 196.8	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2P(=…`
ZINC1550030	0.500	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c…`
ZINC17610743	0.500	347.2 Da LogP -2.50 TPSA 196.8	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2P(…`
ZINC2020098	0.500	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c(…`
ZINC38580950	0.500	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc32)[C@H](O…`
ZINC3869969	0.500	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)…`
ZINC5605239	0.500	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c…`
ZINC6119283	0.500	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)c(…`
ZINC78920152	0.500	364.2 Da LogP -2.45 TPSA 200.2	1 viol.	✓ Clean	`O=c1[nH]c(O)nc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)…`
ZINC8613125	0.500	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c…`
ZINC97973760	0.500	282.3 Da LogP -2.72 TPSA 165.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(=O)[nH]c(N)nc32)[C@@H](…`

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.