Protein profile

VK055_5159

DNA adenine methylase family protein

Genome: KpATCC43816

Gene: dam2 AIK83680.1 Structure source: AlphaFold + ColabFold UniProt A0A9Q8FFK7

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Amino acids 269

Annotations 10

Features 24

PDB binders 0

Druggability 0.932

Overview

Basic information about this protein and its source genome.

Accession: VK055_5159
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: dam2 AIK83680.1
Status: annotated
Amino acids: 269
Structure source: AlphaFold + ColabFold

2.1.1.72

GO:0003676 Binding to a nucleic acid. GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0009007 Catalysis of the reaction: S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine + DNA 6-methylaminopurine. GO:0032259 The process in which a methyl group is covalently attached to a molecule. GO:0032775 OBSOLETE. The covalent transfer of a methyl group to N-6 of adenine in a DNA molecule. GO:1904047 Binding to S-adenosyl-L-methionine.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 42.963
DEG E-value: 7.46e-70
Localization: Unknown
ColabFold pLDDT: 89.56

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 0.932

Structure A0A9Q8FFK7

Pocket Pocket 1

P2Rank 0.846

Structure A0A9Q8FFK7

Pocket Pocket 1

ColabFold model

FPocket 0.855 · Pocket 1

P2Rank 0.868 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 6 / 4744 genomes with a hit

Normalized 0.001

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

2.1.1.72

Gene Ontology (GO)

GO:0003676 Binding to a nucleic acid.
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0009007 Catalysis of the reaction: S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine + DNA 6-methylaminopurine.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.
GO:0032775 OBSOLETE. The covalent transfer of a methyl group to N-6 of adenine in a DNA molecule.
GO:1904047 Binding to S-adenosyl-L-methionine.
GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
GO:0009307 A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
GO:0006298 A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
56	155	Gene3D	G3DSA:1.10.1020.10	-
56	155	InterPro	IPR023095	Adenine-specific methyltransferase, domain 2
3	267	NCBIfam	TIGR00571	Dam family site-specific DNA-(adenine-N6)-methyltransferase
3	267	InterPro	IPR012327	D12 class N6 adenine-specific DNA methyltransferase
1	267	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
1	267	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
177	183	ProSitePatterns	PS00092	N-6 Adenine-specific DNA methylases signature.
177	183	InterPro	IPR002052	DNA methylase, N-6 adenine-specific, conserved site
174	186	PRINTS	PR00505	D12 class N6 adenine-specific DNA methyltransferase signature
174	186	InterPro	IPR012327	D12 class N6 adenine-specific DNA methyltransferase
8	24	PRINTS	PR00505	D12 class N6 adenine-specific DNA methyltransferase signature
8	24	InterPro	IPR012327	D12 class N6 adenine-specific DNA methyltransferase
49	62	PRINTS	PR00505	D12 class N6 adenine-specific DNA methyltransferase signature
49	62	InterPro	IPR012327	D12 class N6 adenine-specific DNA methyltransferase
29	43	PRINTS	PR00505	D12 class N6 adenine-specific DNA methyltransferase signature
29	43	InterPro	IPR012327	D12 class N6 adenine-specific DNA methyltransferase
1	269	PIRSF	PIRSF000398	M_m6A_EcoRV
1	269	InterPro	IPR012263	Adenine modification methylase, M.EcoRV-type
2	267	PANTHER	PTHR30481	DNA ADENINE METHYLASE
2	267	InterPro	IPR012327	D12 class N6 adenine-specific DNA methyltransferase
8	250	Pfam	PF02086	D12 class N6 adenine-specific DNA methyltransferase
8	250	InterPro	IPR012327	D12 class N6 adenine-specific DNA methyltransferase
4	238	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
4	238	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily

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_A0A9Q8FFK7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_5159	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				0.932

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	13.44	0.686
2	1.92	0.039
3	1.44	0.019

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

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	16.88	0.79
2	2.8	0.086
3	0.54	0.0

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.

53 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.

No PDB ligands found through similar proteins.

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL250656	P0AEE8	—	353.4 Da LogP 0.45 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1cccc2c1ncn2[C@@H]1O[C@H](CSCCC(=O)O)[C@@H](O…`
CHEMBL399890	P0AEE8	—	355.4 Da LogP -0.76 TPSA 156.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCCC(=O)O)[C@@H](O…`
SFG	P0AEE8	—	381.4 Da LogP -2.06 TPSA 208.7	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`

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
ZINC13650200	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…`
ZINC205994753	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…`
ZINC205994774	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…`
ZINC27723577	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…`
ZINC38192471	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@@H](N…`
ZINC38192472	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@@H](N)CC[C@@H](…`
ZINC4217451	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@@H](N)CC[C@H](N…`
ZINC12501055	0.818	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…`
ZINC13509082	0.818	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CSCC[C@@H](N)C(=O)O…`
ZINC13509104	0.818	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@@H](N)C(=O)O…`
ZINC1532516	0.818	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CSCC[C@H](N)C(=O)O)…`
ZINC33821012	0.818	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…`
ZINC33821013	0.818	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…`
ZINC4228232	0.818	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…`
ZINC45789230	0.818	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CSCC[C@H](N)C(=O)O…`
ZINC45789233	0.818	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CSCC[C@H](N)C(=O)O)[…`
ZINC13522378	0.796	370.4 Da LogP -1.83 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…`
ZINC13522407	0.796	370.4 Da LogP -1.83 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…`
ZINC256828117	0.796	370.4 Da LogP -1.83 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…`
ZINC256828118	0.796	370.4 Da LogP -1.83 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…`
ZINC5163039	0.745	340.4 Da LogP -0.89 TPSA 145.3	✓ Ro5	✓ Clean	`NCCCSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C…`
ZINC13522400	0.737	400.4 Da LogP -2.42 TPSA 199.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[S@](=O)CC[C@H](N)…`
ZINC13522403	0.737	400.4 Da LogP -2.42 TPSA 199.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[S@@](=O)CC[C@H](N…`
ZINC1775937521	0.726	423.5 Da LogP -1.02 TPSA 194.7	2 viol.	✓ Clean	`CCCN[C@H](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc…`
ZINC95921230	0.726	423.5 Da LogP -1.02 TPSA 194.7	2 viol.	✓ Clean	`CCCN[C@@H](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cn…`
ZINC49014951	0.724	416.4 Da LogP -2.76 TPSA 216.8	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CS(=O)(=O)CC[C@H](N)…`
ZINC49014955	0.724	416.4 Da LogP -2.76 TPSA 216.8	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CS(=O)(=O)CC[C@@H](N…`
ZINC100005972	0.712	400.5 Da LogP -1.54 TPSA 182.6	1 viol.	✓ Clean	`C[S@@H](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC73315766	0.707	381.5 Da LogP 1.73 TPSA 119.3	✓ Ro5	✓ Clean	`CCCCCCCSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](…`
ZINC73315769	0.707	381.5 Da LogP 1.73 TPSA 119.3	✓ Ro5	✓ Clean	`CCCCCCCSC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H]…`
ZINC73315770	0.707	381.5 Da LogP 1.73 TPSA 119.3	✓ Ro5	✓ Clean	`CCCCCCCSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](…`
ZINC73315774	0.707	381.5 Da LogP 1.73 TPSA 119.3	✓ Ro5	✓ Clean	`CCCCCCCSC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H]…`
ZINC12371977	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC12371978	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…`
ZINC13522357	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3…`
ZINC13522362	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC139339614	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c…`
ZINC254297245	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c(…`
ZINC254297254	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c(…`
ZINC254297257	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c(…`
ZINC33821030	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC33821031	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…`
ZINC4214738	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC4228231	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…`
ZINC71755544	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c…`
ZINC71755557	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3…`
ZINC95644663	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC95644664	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…`
ZINC473112262	0.694	397.5 Da LogP -0.92 TPSA 160.4	✓ Ro5	✓ Clean	`CCNC(=O)NCCSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@…`
ZINC526061654	0.694	397.5 Da LogP -0.92 TPSA 160.4	✓ Ro5	✓ Clean	`CCNC(=O)NCCSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[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.