Protein profile

KP13_32230

Formate dehydrogenase H

Genome: KpKP13

Gene: AHE46828.1 Structure source: ColabFold UniProt A0A2U0LLL0

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Amino acids 715

Annotations 10

Features 36

PDB binders 11

Druggability 0.855

Overview

Basic information about this protein and its source genome.

Accession: KP13_32230
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46828.1
Status: annotated
Amino acids: 715
Structure source: 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:0008863 Catalysis of the reaction: formate + NAD+ = CO2 + NADH. 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: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.

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: 96.71

Selected Druggability evidence

ColabFold / curated 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 0.855

Structure CB_KP13_32230

Pocket Pocket 1

P2Rank 0.745

Structure CB_KP13_32230

Pocket Pocket 1

ColabFold model

FPocket 0.855 · Pocket 1

P2Rank 0.745 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 560 / 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: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:0008863 Catalysis of the reaction: formate + NAD+ = CO2 + NADH.
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: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: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.

36 records

Show feature table

Start	End	DB	Term	Name
565	702	SUPERFAMILY	SSF50692	ADC-like
565	702	InterPro	IPR009010	Aspartate decarboxylase-like domain superfamily
1	56	ProSiteProfiles	PS51669	Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile.
1	56	InterPro	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain
2	688	PANTHER	PTHR43105	RESPIRATORY NITRATE REDUCTASE
1	53	Pfam	PF04879	Molybdopterin oxidoreductase Fe4S4 domain
1	53	InterPro	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain
140	334	FunFam	G3DSA:3.40.228.10:FF:000002	Formate dehydrogenase subunit alpha
6	685	NCBIfam	TIGR01591	formate dehydrogenase subunit alpha
6	685	InterPro	IPR006478	Formate dehydrogenase, alpha subunit
540	692	PIRSF	PIRSF000144	CbbBc
53	444	PIRSF	PIRSF000144	CbbBc
615	642	ProSitePatterns	PS00932	Prokaryotic molybdopterin oxidoreductases signature 3.
615	642	InterPro	IPR006655	Molybdopterin oxidoreductase, prokaryotic, conserved site
140	334	Gene3D	G3DSA:3.40.228.10	Dimethylsulfoxide Reductase, domain 2
576	682	Pfam	PF01568	Molydopterin dinucleotide binding domain
576	682	InterPro	IPR006657	Molybdopterin dinucleotide-binding domain
61	487	Pfam	PF00384	Molybdopterin oxidoreductase
61	487	InterPro	IPR006656	Molybdopterin oxidoreductase
689	715	Gene3D	G3DSA:1.20.5.460	Single helix bin
571	687	CDD	cd02790	MopB_CT_Formate-Dh_H
571	687	InterPro	IPR041925	Formate dehydrogenase H, molybdopterin-binding domain
433	450	ProSitePatterns	PS00490	Prokaryotic molybdopterin oxidoreductases signature 2.
433	450	InterPro	IPR006655	Molybdopterin oxidoreductase, prokaryotic, conserved site
73	530	Gene3D	G3DSA:3.40.50.740	-
6	23	ProSitePatterns	PS00551	Prokaryotic molybdopterin oxidoreductases signature 1.
6	23	InterPro	IPR027467	Molybdopterin oxidoreductase, molybdopterin cofactor binding site
572	688	Gene3D	G3DSA:2.40.40.20	-
1	54	SMART	SM00926	Molybdop_Fe4S4_2
1	54	InterPro	IPR006963	Molybdopterin oxidoreductase, 4Fe-4S domain
6	564	CDD	cd02753	MopB_Formate-Dh-H
6	564	InterPro	IPR041924	Formate dehydrogenase H, N-terminal
572	688	FunFam	G3DSA:2.40.40.20:FF:000011	Formate dehydrogenase, alpha subunit
1	55	FunFam	G3DSA:2.20.25.90:FF:000001	Formate dehydrogenase subunit alpha
1	563	SUPERFAMILY	SSF53706	Formate dehydrogenase/DMSO reductase, domains 1-3
1	55	Gene3D	G3DSA:2.20.25.90	-

3D Structure

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

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
ColabFold KP13_32230	ColabFold	—	—	full sequence	—	Viewing

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				0.855
4				0.541

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	10.93	0.586
2	9.62	0.517
3	6.07	0.3
4	3.54	0.131
5	3.54	0.13

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
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	1FDI	P07658	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	1AA6	P07658	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-]`
W	1H0H	Q934F5	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
ZINC104869865	0.689	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	0.689	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	0.689	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	0.689	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	0.689	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	0.689	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	0.689	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	0.635	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	0.635	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	0.635	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	0.635	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	0.635	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	0.635	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	0.635	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	0.635	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	0.635	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)[…`
ZINC71774763	0.585	432.3 Da LogP -2.23 TPSA 198.3	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@](=O)(O)N3CCOCC3…`
ZINC100058967	0.570	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	0.570	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	0.570	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	0.570	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(…`
ZINC106686432	0.544	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	0.544	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	0.544	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	0.544	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	0.544	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	0.544	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…`
ZINC4743771	0.544	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	0.544	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	0.544	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	0.544	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…`
ZINC80601236	0.544	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	0.544	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	0.537	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	0.537	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…`
ZINC1550030	0.520	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…`
ZINC1698205	0.520	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…`
ZINC2020098	0.520	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(…`
ZINC3869967	0.520	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…`
ZINC3869969	0.520	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)…`
ZINC3869970	0.520	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…`
ZINC4990800	0.520	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](…`
ZINC4990801	0.520	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](…`
ZINC5605239	0.520	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…`
ZINC8613125	0.520	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…`
ZINC97973759	0.520	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…`

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.