Protein profile

KP13_00162

ATP-dependent DNA helicase recG

Genome: KpKP13

Gene: recG AHE42082.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H4K6

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Amino acids 693

Annotations 9

Features 38

PDB binders 2

Druggability 0.673

Overview

Basic information about this protein and its source genome.

Accession: KP13_00162
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: recG AHE42082.1
Status: annotated
Amino acids: 693
Structure source: AlphaFold + ColabFold

5.6.2.4

GO:0003676 Binding to a nucleic acid. GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis. GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction. GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0043138 Unwinding a DNA helix in the direction 5' to 3', driven by ATP hydrolysis.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 37.975
Human E-value: 4.92e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 94.661
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 85.59

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 0.673

Structure A0A0H3H4K6

Pocket Pocket 25

P2Rank 0.893

Structure A0A0H3H4K6

Pocket Pocket 1

ColabFold model

FPocket 0.881 · Pocket 4

P2Rank 0.874 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 185 / 4744 genomes with a hit

Normalized 0.039

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

5.6.2.4

Gene Ontology (GO)

GO:0003676 Binding to a nucleic acid.
GO:0003678 Unwinding of a DNA helix, driven by ATP hydrolysis.
GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0043138 Unwinding a DNA helix in the direction 5' to 3', driven by ATP hydrolysis.
GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Sequence Features

Domain/signature hits from InterPro and related databases.

38 records

Show feature table

Start	End	DB	Term	Name
457	615	CDD	cd18811	SF2_C_RecG
208	450	FunFam	G3DSA:3.40.50.300:FF:000715	ATP-dependent DNA helicase RecG
617	672	Pfam	PF19833	ATP-dependent DNA helicase RecG, domain 3, C-terminal
617	672	InterPro	IPR045562	ATP-dependent DNA helicase RecG, domain 3, C-terminal
265	459	SMART	SM00487	ultradead3
265	459	InterPro	IPR014001	Helicase superfamily 1/2, ATP-binding domain
482	628	ProSiteProfiles	PS51194	Superfamilies 1 and 2 helicase C-terminal domain profile.
482	628	InterPro	IPR001650	Helicase, C-terminal
480	588	Pfam	PF00271	Helicase conserved C-terminal domain
480	588	InterPro	IPR001650	Helicase, C-terminal
209	453	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
209	453	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
63	135	CDD	cd04488	RecG_wedge_OBF
15	171	Pfam	PF17191	RecG wedge domain
15	171	InterPro	IPR033454	RecG, wedge domain
292	653	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
292	653	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
224	452	CDD	cd17992	DEXHc_RecG
5	684	PANTHER	PTHR47964	ATP-DEPENDENT DNA HELICASE HOMOLOG RECG, CHLOROPLASTIC
5	684	InterPro	IPR047112	ATP-dependent DNA helicase RecG/Transcription-repair-coupling factor
505	589	SMART	SM00490	helicmild6
505	589	InterPro	IPR001650	Helicase, C-terminal
47	140	FunFam	G3DSA:2.40.50.140:FF:000134	ATP-dependent DNA helicase RecG
9	175	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
9	175	InterPro	IPR012340	Nucleic acid-binding, OB-fold
28	664	NCBIfam	TIGR00643	ATP-dependent DNA helicase RecG
28	664	InterPro	IPR004609	ATP-dependent DNA helicase RecG
457	630	FunFam	G3DSA:3.40.50.300:FF:000391	ATP-dependent DNA helicase RecG
208	450	Gene3D	G3DSA:3.40.50.300	-
208	450	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
47	140	Gene3D	G3DSA:2.40.50.140	-
47	140	InterPro	IPR012340	Nucleic acid-binding, OB-fold
293	433	Pfam	PF00270	DEAD/DEAH box helicase
293	433	InterPro	IPR011545	DEAD/DEAH box helicase domain
283	448	ProSiteProfiles	PS51192	Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
283	448	InterPro	IPR014001	Helicase superfamily 1/2, ATP-binding domain
457	630	Gene3D	G3DSA:3.40.50.300	-
457	630	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase

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_A0A0H3H4K6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00162	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
25				0.673
49				0.391

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	16.98	0.793
2	15.91	0.765
3	3.83	0.149
4	1.42	0.018

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				0.881
9				0.212

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	16.18	0.772
2	7.37	0.385
3	2.41	0.065
4	2.3	0.059
5	1.98	0.042

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.

57 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
AGS	6QV4	G0S0B9	523.2 Da LogP -1.51 TPSA 262.1	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
ANP	6L5N	Q9NR30	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`

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
CHEMBL1471192	P46063	7.25	451.6 Da LogP 1.73 TPSA 104.8	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)NCC(=O)N(CC(=O)NC2CCCCC2)CC2CCC…`
CHEMBL1560762	P46063	6.85	396.5 Da LogP 1.97 TPSA 93.7	✓ Ro5	✓ Clean	`O=C(COc1ccc(S(=O)(=O)NC2CCCCC2)cc1)NCC1CCCO1`
CHEMBL1446521	P46063	6.50	346.5 Da LogP 2.18 TPSA 69.0	✓ Ro5	✓ Clean	`Cc1ccc(-c2nnc(SCC(=O)NCC3CCCO3)n2C)cc1`
CHEMBL1448630	P46063	6.05	294.4 Da LogP 1.48 TPSA 59.6	✓ Ro5	✓ Clean	`COc1ccc(C(=O)NC(=S)NCC2CCCO2)cc1`
CHEMBL1057	P46063	—	332.3 Da LogP 3.67 TPSA 76.0	✓ Ro5	✓ Clean	`O=C1OC2(c3ccc(O)cc3Oc3cc(O)ccc32)c2ccccc21`

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
ZINC316109	1.000	294.4 Da LogP 1.48 TPSA 59.6	✓ Ro5	✓ Clean	`COc1ccc(C(=O)NC(=S)NC[C@H]2CCCO2)cc1`
ZINC316110	1.000	294.4 Da LogP 1.48 TPSA 59.6	✓ Ro5	✓ Clean	`COc1ccc(C(=O)NC(=S)NC[C@@H]2CCCO2)cc1`
ZINC3286414	1.000	346.5 Da LogP 2.18 TPSA 69.0	✓ Ro5	✓ Clean	`Cc1ccc(-c2nnc(SCC(=O)NC[C@H]3CCCO3)n2C)cc1`
ZINC3286415	1.000	346.5 Da LogP 2.18 TPSA 69.0	✓ Ro5	✓ Clean	`Cc1ccc(-c2nnc(SCC(=O)NC[C@@H]3CCCO3)n2C)cc1`
ZINC3860453	1.000	332.3 Da LogP 3.67 TPSA 76.0	✓ Ro5	✓ Clean	`O=C1OC2(c3ccc(O)cc3Oc3cc(O)ccc32)c2ccccc21`
ZINC798668	1.000	396.5 Da LogP 1.97 TPSA 93.7	✓ Ro5	✓ Clean	`O=C(COc1ccc(S(=O)(=O)NC2CCCCC2)cc1)NC[C@H]1CCCO1`
ZINC798669	1.000	396.5 Da LogP 1.97 TPSA 93.7	✓ Ro5	✓ Clean	`O=C(COc1ccc(S(=O)(=O)NC2CCCCC2)cc1)NC[C@@H]1CCC…`
ZINC804908	0.979	382.5 Da LogP 1.58 TPSA 93.7	✓ Ro5	✓ Clean	`O=C(COc1ccc(S(=O)(=O)NC2CCCC2)cc1)NC[C@H]1CCCO1`
ZINC804909	0.979	382.5 Da LogP 1.58 TPSA 93.7	✓ Ro5	✓ Clean	`O=C(COc1ccc(S(=O)(=O)NC2CCCC2)cc1)NC[C@@H]1CCCO1`
ZINC3485814	0.870	366.9 Da LogP 2.52 TPSA 69.0	✓ Ro5	✓ Clean	`Cn1c(SCC(=O)NC[C@H]2CCCO2)nnc1-c1ccc(Cl)cc1`
ZINC3485816	0.870	366.9 Da LogP 2.52 TPSA 69.0	✓ Ro5	✓ Clean	`Cn1c(SCC(=O)NC[C@@H]2CCCO2)nnc1-c1ccc(Cl)cc1`
ZINC6914139	0.870	350.4 Da LogP 2.01 TPSA 69.0	✓ Ro5	✓ Clean	`Cn1c(SCC(=O)NC[C@@H]2CCCO2)nnc1-c1ccc(F)cc1`
ZINC6914143	0.870	350.4 Da LogP 2.01 TPSA 69.0	✓ Ro5	✓ Clean	`Cn1c(SCC(=O)NC[C@H]2CCCO2)nnc1-c1ccc(F)cc1`
ZINC3402375	0.855	388.5 Da LogP 3.17 TPSA 69.0	✓ Ro5	✓ Clean	`Cn1c(SCC(=O)NC[C@H]2CCCO2)nnc1-c1ccc(C(C)(C)C)c…`
ZINC3402380	0.855	388.5 Da LogP 3.17 TPSA 69.0	✓ Ro5	✓ Clean	`Cn1c(SCC(=O)NC[C@@H]2CCCO2)nnc1-c1ccc(C(C)(C)C)…`
ZINC4806433	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC43199396	0.842	331.3 Da LogP 3.54 TPSA 81.8	✓ Ro5	✓ Clean	`Nc1ccc2c(c1)Oc1cc(O)ccc1[C@]21OC(=O)c2ccccc21`
ZINC43199397	0.842	331.3 Da LogP 3.54 TPSA 81.8	✓ Ro5	✓ Clean	`Nc1ccc2c(c1)Oc1cc(O)ccc1[C@@]21OC(=O)c2ccccc21`
ZINC880963	0.839	362.5 Da LogP 1.88 TPSA 78.3	✓ Ro5	✓ Clean	`COc1ccc(-c2nnc(SCC(=O)NC[C@H]3CCCO3)n2C)cc1`
ZINC880965	0.839	362.5 Da LogP 1.88 TPSA 78.3	✓ Ro5	✓ Clean	`COc1ccc(-c2nnc(SCC(=O)NC[C@@H]3CCCO3)n2C)cc1`
ZINC12360002	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC2207000	0.810	403.5 Da LogP 2.22 TPSA 98.1	✓ Ro5	✓ Clean	`CCC(=O)Nc1ccc(-c2nnc(SCC(=O)NC[C@H]3CCCO3)n2C)c…`
ZINC2207001	0.810	403.5 Da LogP 2.22 TPSA 98.1	✓ Ro5	✓ Clean	`CCC(=O)Nc1ccc(-c2nnc(SCC(=O)NC[C@@H]3CCCO3)n2C)…`
ZINC31977053	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC53683898	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC3286424	0.786	422.6 Da LogP 3.94 TPSA 69.0	✓ Ro5	✓ Clean	`Cc1ccc(-c2nnc(SCC(=O)NC[C@H]3CCCO3)n2-c2ccc(C)c…`
ZINC3286426	0.786	422.6 Da LogP 3.94 TPSA 69.0	✓ Ro5	✓ Clean	`Cc1ccc(-c2nnc(SCC(=O)NC[C@@H]3CCCO3)n2-c2ccc(C)…`
ZINC15020070	0.780	346.3 Da LogP 3.97 TPSA 65.0	✓ Ro5	✓ Clean	`COc1ccc2c(c1)Oc1cc(O)ccc1[C@@]21OC(=O)c2ccccc21`
ZINC15020073	0.780	346.3 Da LogP 3.97 TPSA 65.0	✓ Ro5	✓ Clean	`COc1ccc2c(c1)Oc1cc(O)ccc1[C@]21OC(=O)c2ccccc21`
ZINC9193273	0.780	386.5 Da LogP 2.75 TPSA 69.0	✓ Ro5	✓ Clean	`Cn1c(SCC(=O)NC[C@@H]2CCCO2)nnc1-c1ccc2c(c1)CCCC2`
ZINC9193274	0.780	386.5 Da LogP 2.75 TPSA 69.0	✓ Ro5	✓ Clean	`Cn1c(SCC(=O)NC[C@H]2CCCO2)nnc1-c1ccc2c(c1)CCCC2`
ZINC335097	0.778	235.3 Da LogP 1.60 TPSA 47.6	✓ Ro5	✓ Clean	`COc1ccc(C(=O)NC[C@H]2CCCO2)cc1`
ZINC335098	0.778	235.3 Da LogP 1.60 TPSA 47.6	✓ Ro5	✓ Clean	`COc1ccc(C(=O)NC[C@@H]2CCCO2)cc1`
ZINC301598	0.766	278.4 Da LogP 1.78 TPSA 50.4	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)NC(=S)NC[C@H]2CCCO2)cc1`
ZINC301599	0.766	278.4 Da LogP 1.78 TPSA 50.4	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)NC(=S)NC[C@@H]2CCCO2)cc1`
ZINC14183634	0.763	333.4 Da LogP 1.26 TPSA 81.9	✓ Ro5	✓ Clean	`Cn1c(SCC(=O)NC[C@@H]2CCCO2)nnc1-c1cccnc1`
ZINC14183635	0.763	333.4 Da LogP 1.26 TPSA 81.9	✓ Ro5	✓ Clean	`Cn1c(SCC(=O)NC[C@H]2CCCO2)nnc1-c1cccnc1`
ZINC5861269	0.754	346.5 Da LogP 2.18 TPSA 69.0	✓ Ro5	✓ Clean	`Cc1ccccc1-c1nnc(SCC(=O)NC[C@@H]2CCCO2)n1C`
ZINC5861281	0.754	346.5 Da LogP 2.18 TPSA 69.0	✓ Ro5	✓ Clean	`Cc1ccccc1-c1nnc(SCC(=O)NC[C@H]2CCCO2)n1C`
ZINC358808	0.750	320.5 Da LogP 2.77 TPSA 50.4	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc(C(=O)NC(=S)NC[C@H]2CCCO2)cc1`
ZINC358809	0.750	320.5 Da LogP 2.77 TPSA 50.4	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc(C(=O)NC(=S)NC[C@@H]2CCCO2)cc1`
ZINC798731	0.745	356.4 Da LogP 1.05 TPSA 93.7	✓ Ro5	✓ Clean	`CC(C)NS(=O)(=O)c1ccc(OCC(=O)NC[C@@H]2CCCO2)cc1`
ZINC810031	0.745	394.5 Da LogP 2.53 TPSA 84.5	✓ Ro5	✓ Clean	`O=C(CCc1ccc(S(=O)(=O)NC2CCCCC2)cc1)NC[C@@H]1CCC…`

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.