Protein profile

KP13_04385

ATP-independent RNA helicase dbpA

Genome: KpKP13

Gene: AHE44883.1 dbpA Structure source: AlphaFold + ColabFold UniProt A0A0H3GSK5

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Amino acids 457

Annotations 9

Features 37

PDB binders 6

Druggability 0.797

Overview

Basic information about this protein and its source genome.

Accession: KP13_04385
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44883.1 dbpA
Status: annotated
Amino acids: 457
Structure source: AlphaFold + ColabFold

3.6.4.13

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0003676 Binding to a nucleic acid. GO:0003724 Unwinding of an RNA helix, driven by ATP hydrolysis. GO:0000027 The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0034458 Unwinding of an RNA helix in the 3' to 5' direction, driven by ATP hydrolysis.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 50.538
Human E-value: 6.29e-20
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 42.049
DEG E-value: 1.11e-87
Localization: Cytoplasmic
ColabFold pLDDT: 93.52

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 0.797

Structure A0A0H3GSK5

Pocket Pocket 2

P2Rank 0.67

Structure A0A0H3GSK5

Pocket Pocket 1

ColabFold model

FPocket 0.323 · Pocket 35

P2Rank 0.827 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 142 / 4744 genomes with a hit

Normalized 0.03

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)

3.6.4.13

Gene Ontology (GO)

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0003676 Binding to a nucleic acid.
GO:0003724 Unwinding of an RNA helix, driven by ATP hydrolysis.
GO:0000027 The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0034458 Unwinding of an RNA helix in the 3' to 5' direction, 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:0003723 Binding to an RNA molecule or a portion thereof.

Sequence Features

Domain/signature hits from InterPro and related databases.

37 records

Show feature table

Start	End	DB	Term	Name
34	205	ProSiteProfiles	PS51192	Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
34	205	InterPro	IPR014001	Helicase superfamily 1/2, ATP-binding domain
15	206	CDD	cd00268	DEADc
32	457	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
212	365	Gene3D	G3DSA:3.40.50.300	-
212	365	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
1	2	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
212	379	FunFam	G3DSA:3.40.50.300:FF:001245	ATP-dependent RNA helicase DbpA
216	345	CDD	cd18787	SF2_C_DEAD
384	454	Pfam	PF03880	DbpA RNA binding domain
384	454	InterPro	IPR005580	DEAD box helicase DbpA/CsdA, RNA-binding domain
22	219	SMART	SM00487	ultradead3
22	219	InterPro	IPR014001	Helicase superfamily 1/2, ATP-binding domain
3	358	PANTHER	PTHR47959	ATP-DEPENDENT RNA HELICASE RHLE-RELATED
228	336	Pfam	PF00271	Helicase conserved C-terminal domain
228	336	InterPro	IPR001650	Helicase, C-terminal
14	31	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
27	190	Pfam	PF00270	DEAD/DEAH box helicase
27	190	InterPro	IPR011545	DEAD/DEAH box helicase domain
1	208	Gene3D	G3DSA:3.40.50.300	-
1	208	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
151	159	ProSitePatterns	PS00039	DEAD-box subfamily ATP-dependent helicases signature.
151	159	InterPro	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site
1	31	Phobius	SIGNAL_PEPTIDE	Signal peptide region
384	456	Gene3D	G3DSA:3.30.70.330	-
384	456	InterPro	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily
5	457	Hamap	MF_00965	ATP-dependent RNA helicase DbpA [dbpA].
5	457	InterPro	IPR028619	ATP-dependent RNA helicase DbpA
72	350	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
72	350	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
255	336	SMART	SM00490	helicmild6
255	336	InterPro	IPR001650	Helicase, C-terminal
384	456	FunFam	G3DSA:3.30.70.330:FF:000254	ATP-dependent RNA helicase DbpA
384	456	CDD	cd12501	RRM_EcDbpA_like
231	375	ProSiteProfiles	PS51194	Superfamilies 1 and 2 helicase C-terminal domain profile.
231	375	InterPro	IPR001650	Helicase, C-terminal
3	13	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.

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_A0A0H3GSK5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04385	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				0.797

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	7.49	0.394
2	4.61	0.199
3	3.84	0.149
4	1.53	0.023

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
35				0.323

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	11.43	0.61
2	3.4	0.122
3	3.33	0.118
4	2.01	0.043
5	1.31	0.014

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.

56 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
8OD	3NBF	Q72GF3	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`c1nc(c2c(n1)N(C(=O)N2)[C@H]3[C@@H]([C@@H]([C@H]…`
8OP	3MWK	Q72GF3	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`c1nc(c2c(n1)N(C(=O)N2)[C@H]3[C@@H]([C@@H]([C@H]…`
8OX	3MWL	Q72GF3	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`c1nc(c2c(n1)N(C(=O)N2)[C@H]3[C@@H]([C@@H]([C@H]…`
AF3	3EX7	P38919	84.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`F[Al](F)F`
ANP	4D25	O01378	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)…`
LMR	5GVR	Q9UJV9	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@@H](C(=O)O)O)C(=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
ZINC17376093	1.000	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=O)n2[C@@H]1O[C@H](CO)[C@@H](O)…`
ZINC5163021	1.000	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=O)n2[C@@H]1O[C@H](CO)[C@@H](O)…`
ZINC80023117	1.000	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=O)n2[C@@H]1O[C@H](CO)[C@H](O)[…`
ZINC80023118	1.000	283.2 Da LogP -2.69 TPSA 159.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=O)n2[C@@H]1O[C@H](CO)[C@H](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)(…`
ZINC104199549	0.771	265.2 Da LogP -1.64 TPSA 131.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=O)n2[C@H]1O[C@@H](CO)[C@@H]2O[…`
ZINC104199552	0.771	265.2 Da LogP -1.64 TPSA 131.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=O)n2[C@@H]1O[C@@H](CO)[C@@H]2O…`
ZINC1566227	0.771	265.2 Da LogP -1.64 TPSA 131.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=O)n2[C@H]1O[C@@H](CO)[C@@H]2O[…`
ZINC5389846	0.771	265.2 Da LogP -1.64 TPSA 131.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=O)n2[C@@H]1O[C@@H](CO)[C@@H]2O…`
ZINC17376092	0.755	299.3 Da LogP -1.32 TPSA 142.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=S)n2[C@@H]1O[C@H](CO)[C@@H](O)…`
ZINC33837666	0.755	299.3 Da LogP -1.32 TPSA 142.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=S)n2[C@@H]1O[C@H](CO)[C@H](O)[…`
ZINC4823533	0.755	299.3 Da LogP -1.32 TPSA 142.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=S)n2[C@H]1O[C@@H](CO)[C@@H](O)…`
ZINC4823535	0.755	299.3 Da LogP -1.32 TPSA 142.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=S)n2[C@H]1O[C@@H](CO)[C@@H](O)…`
ZINC4823537	0.755	299.3 Da LogP -1.32 TPSA 142.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=S)n2[C@@H]1O[C@@H](CO)[C@@H](O…`
ZINC5395342	0.755	299.3 Da LogP -1.32 TPSA 142.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1[nH]c(=S)n2[C@@H]1O[C@H](CO)[C@H](O)[…`
ZINC71773889	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@H](O)C(=O)O`
ZINC71773890	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC71773891	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC12360002	0.651	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	0.651	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	0.651	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC31977053	0.651	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.651	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	0.651	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.651	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	0.651	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.651	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	0.651	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC5390312	0.643	350.3 Da LogP -2.85 TPSA 192.4	1 viol.	✓ Clean	`Nc1ncnc2c1c1c(=O)[nH]c(=O)[nH]c1n2[C@H]1O[C@@H]…`
ZINC5390313	0.643	350.3 Da LogP -2.85 TPSA 192.4	1 viol.	✓ Clean	`Nc1ncnc2c1c1c(=O)[nH]c(=O)[nH]c1n2[C@@H]1O[C@@H…`
ZINC5390314	0.643	350.3 Da LogP -2.85 TPSA 192.4	1 viol.	✓ Clean	`Nc1ncnc2c1c1c(=O)[nH]c(=O)[nH]c1n2[C@H]1O[C@@H]…`
ZINC5390315	0.643	350.3 Da LogP -2.85 TPSA 192.4	1 viol.	✓ Clean	`Nc1ncnc2c1c1c(=O)[nH]c(=O)[nH]c1n2[C@@H]1O[C@@H…`
ZINC12378687	0.635	299.2 Da LogP -3.39 TPSA 179.5	1 viol.	✓ Clean	`Nc1nc2c([nH]c(=O)n2[C@@H]2O[C@H](CO)[C@H](O)[C@…`
ZINC8830749	0.635	299.2 Da LogP -3.39 TPSA 179.5	1 viol.	✓ Clean	`Nc1nc2c([nH]c(=O)n2[C@@H]2O[C@H](CO)[C@H](O)[C@…`
ZINC8830750	0.635	299.2 Da LogP -3.39 TPSA 179.5	1 viol.	✓ Clean	`Nc1nc2c([nH]c(=O)n2[C@@H]2O[C@@H](CO)[C@H](O)[C…`
ZINC8830751	0.635	299.2 Da LogP -3.39 TPSA 179.5	1 viol.	✓ Clean	`Nc1nc2c([nH]c(=O)n2[C@@H]2O[C@H](CO)[C@@H](O)[C…`
ZINC8830752	0.635	299.2 Da LogP -3.39 TPSA 179.5	1 viol.	✓ Clean	`Nc1nc2c([nH]c(=O)n2[C@@H]2O[C@@H](CO)[C@@H](O)[…`
ZINC8952459	0.635	299.2 Da LogP -3.39 TPSA 179.5	1 viol.	✓ Clean	`Nc1nc2c([nH]c(=O)n2[C@@H]2O[C@H](CO)[C@@H](O)[C…`
ZINC5082171	0.618	297.3 Da LogP -2.85 TPSA 149.4	✓ Ro5	✓ Clean	`Cn1cnc2c([nH]c(=O)n2[C@H]2O[C@@H](CO)[C@@H](O)[…`
ZINC5082172	0.618	297.3 Da LogP -2.85 TPSA 149.4	✓ Ro5	✓ Clean	`Cn1cnc2c([nH]c(=O)n2[C@@H]2O[C@@H](CO)[C@@H](O)…`
ZINC17064639	0.614	349.3 Da LogP -2.56 TPSA 198.4	2 viol.	✓ Clean	`Nc1nc(=O)c2c3c(N)ncnc3n([C@@H]3O[C@@H](CO)[C@@H…`
ZINC17064641	0.614	349.3 Da LogP -2.56 TPSA 198.4	2 viol.	✓ Clean	`Nc1nc(=O)c2c3c(N)ncnc3n([C@H]3O[C@@H](CO)[C@@H]…`
ZINC5385128	0.614	349.3 Da LogP -2.56 TPSA 198.4	2 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)c1c(N)ncnc1n2[C@H]1O[C@@H](C…`
ZINC5385129	0.614	349.3 Da LogP -2.56 TPSA 198.4	2 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)c1c(N)ncnc1n2[C@@H]1O[C@@H](…`
ZINC4830734	0.611	297.3 Da LogP -2.68 TPSA 148.7	✓ Ro5	✓ Clean	`Cn1c(=O)n([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c2n…`
ZINC4830735	0.611	297.3 Da LogP -2.68 TPSA 148.7	✓ Ro5	✓ Clean	`Cn1c(=O)n([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c2…`
ZINC4830736	0.611	297.3 Da LogP -2.68 TPSA 148.7	✓ Ro5	✓ Clean	`Cn1c(=O)n([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c2…`
ZINC4830737	0.611	297.3 Da LogP -2.68 TPSA 148.7	✓ Ro5	✓ Clean	`Cn1c(=O)n([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c…`
ZINC4823726	0.596	282.3 Da LogP -2.40 TPSA 165.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1nc(N)n2[C@H]1O[C@@H](CO)[C@@H](O)[C@H…`
ZINC4823727	0.596	282.3 Da LogP -2.40 TPSA 165.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1nc(N)n2[C@@H]1O[C@@H](CO)[C@@H](O)[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.