Protein profile

VK055_3909

csdA, DEAD-box RNA helicase

Genome: KpATCC43816

Gene: AIK82457.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTN8

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Amino acids 643

Annotations 13

Features 42

PDB binders 8

Druggability 0.46

Overview

Basic information about this protein and its source genome.

Accession: VK055_3909
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK82457.1
Status: annotated
Amino acids: 643
Structure source: AlphaFold + ColabFold

3.6.4.13

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0016817 Catalysis of the hydrolysis of any acid anhydride. GO:0003676 Binding to a nucleic acid. GO:0003724 Unwinding of an RNA helix, driven by ATP hydrolysis. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0000027 The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 50.847
Human E-value: 6.23e-12
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 92.691
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 79.03

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 0.46

Structure A0A0H3GTN8

Pocket Pocket 8

P2Rank 0.784

Structure A0A0H3GTN8

Pocket Pocket 1

ColabFold model

FPocket 0.149 · Pocket 51

P2Rank 0.537 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 146 / 4744 genomes with a hit

Normalized 0.031

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 12 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:0016817 Catalysis of the hydrolysis of any acid anhydride.
GO:0003676 Binding to a nucleic acid.
GO:0003724 Unwinding of an RNA helix, driven by ATP hydrolysis.
GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0000027 The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.
GO:0070417 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
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:0033592 An activity that facilitates the formation of a complementary double-stranded RNA molecule.
GO:0006401 The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.

Sequence Features

Domain/signature hits from InterPro and related databases.

42 records

Show feature table

Start	End	DB	Term	Name
491	560	Pfam	PF03880	DbpA RNA binding domain
491	560	InterPro	IPR005580	DEAD box helicase DbpA/CsdA, RNA-binding domain
1	562	Hamap	MF_00964	ATP-dependent RNA helicase DeaD [deaD].
1	562	InterPro	IPR028618	ATP-dependent RNA helicase DeaD
558	643	MobiDBLite	mobidb-lite	consensus disorder prediction
215	436	FunFam	G3DSA:3.40.50.300:FF:000374	ATP-dependent RNA helicase DeaD
220	349	CDD	cd18787	SF2_C_DEAD
585	643	Pfam	PF12343	DeaD helicase C-terminal disordered region
585	643	InterPro	IPR021046	Cold-shock protein, DEAD box A, C-terminal
75	361	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
75	361	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
446	482	MobiDBLite	mobidb-lite	consensus disorder prediction
2	211	Gene3D	G3DSA:3.40.50.300	-
2	211	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
31	195	Pfam	PF00270	DEAD/DEAH box helicase
31	195	InterPro	IPR011545	DEAD/DEAH box helicase domain
154	162	ProSitePatterns	PS00039	DEAD-box subfamily ATP-dependent helicases signature.
154	162	InterPro	IPR000629	ATP-dependent RNA helicase DEAD-box, conserved site
6	211	FunFam	G3DSA:3.40.50.300:FF:000108	ATP-dependent RNA helicase RhlE
25	223	SMART	SM00487	ultradead3
25	223	InterPro	IPR014001	Helicase superfamily 1/2, ATP-binding domain
259	340	SMART	SM00490	helicmild6
259	340	InterPro	IPR001650	Helicase, C-terminal
37	208	ProSiteProfiles	PS51192	Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile.
37	208	InterPro	IPR014001	Helicase superfamily 1/2, ATP-binding domain
6	34	ProSiteProfiles	PS51195	DEAD-box RNA helicase Q motif profile.
6	34	InterPro	IPR014014	RNA helicase, DEAD-box type, Q motif
490	562	CDD	cd12499	RRM_EcCsdA_like
490	562	InterPro	IPR034415	CsdA, RNA recognition motif
214	438	Gene3D	G3DSA:3.40.50.300	-
214	438	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
5	604	PANTHER	PTHR47963	DEAD-BOX ATP-DEPENDENT RNA HELICASE 47, MITOCHONDRIAL
232	379	ProSiteProfiles	PS51194	Superfamilies 1 and 2 helicase C-terminal domain profile.
232	379	InterPro	IPR001650	Helicase, C-terminal
17	209	CDD	cd00268	DEADc
232	340	Pfam	PF00271	Helicase conserved C-terminal domain
232	340	InterPro	IPR001650	Helicase, C-terminal
491	561	Gene3D	G3DSA:3.30.70.330	-
491	561	InterPro	IPR012677	Nucleotide-binding alpha-beta plait domain superfamily
439	482	MobiDBLite	mobidb-lite	consensus disorder prediction
569	643	MobiDBLite	mobidb-lite	consensus disorder prediction
490	562	FunFam	G3DSA:3.30.70.330:FF:000068	ATP-dependent RNA helicase DeaD

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_A0A0H3GTN8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3909	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
15				0.123
53				0.093
47				0.006
55				0.0

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	19.89	0.784
2	4.22	0.142
3	3.3	0.092
4	1.26	0.011
5	1.01	0.005

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
51				0.149
1				0.0
45				0.0
50				0.0

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	11.69	0.537
2	6.58	0.28
3	1.2	0.009
4	1.18	0.009
5	1.17	0.009

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.

58 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	2DB3	P09052	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)…`
CXS	4NHO	Q9BUQ8	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCCS(=O)(=O)O`
IHP	6QX9	Q9BUQ8	660.0 Da LogP -3.13 TPSA 400.6	3 viol.	✓ Clean	`C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O…`
M7M	6QX9	Q9BUQ8	487.3 Da LogP -2.28 TPSA 218.4	2 viol.	✓ Clean	`CN1CN(C2=C1C(=O)N=C(N2)N(C)C)[C@H]3[C@@H]([C@@H…`

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
ZINC2004372	1.000	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.926	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
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)(…`
ZINC1710230	0.786	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC113264413	0.778	317.4 Da LogP 3.98 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccc(-c3ccccc3)cc2)cc1)C(=O)O`
ZINC113264415	0.778	317.4 Da LogP 3.98 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(-c2ccc(-c3ccccc3)cc2)cc1)C(=O)O`
ZINC2244337	0.778	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccccc2)cc1)C(=O)O`
ZINC2244338	0.778	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(-c2ccccc2)cc1)C(=O)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…`
ZINC1834294	0.769	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(C[C@H](N)C(=O)O)c1)C(=O)O`
ZINC1834295	0.769	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(C[C@@H](N)C(=O)O)c1)C(=O)O`
ZINC1834297	0.769	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](Cc1cccc(C[C@@H](N)C(=O)O)c1)C(=O)O`
ZINC13518964	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC39351856	0.731	328.4 Da LogP 1.26 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccc(C[C@H](N)C(=O)O)cc2)cc1)C…`
ZINC4096224	0.729	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC2561081	0.724	269.3 Da LogP 1.87 TPSA 80.4	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(C(=O)c2ccccc2)cc1)C(=O)O`
ZINC2561082	0.724	269.3 Da LogP 1.87 TPSA 80.4	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(C(=O)c2ccccc2)cc1)C(=O)O`
ZINC13556870	0.722	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@@H](O)[C@@H](O)[C@H](O)[C@@H…`
ZINC71789368	0.722	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](OP(=O)(O)O)[C@@H](O)[C@H]…`
ZINC71792243	0.722	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](O)[C@@H](O)[C@@H…`
ZINC105372833	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC105372837	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC17107643	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.712	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC100015956	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](OP(=O)(O)O)[C@H]…`
ZINC100015959	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@@H](OP(=O)(O)O)[C@H]…`
ZINC100016166	0.706	340.1 Da LogP -3.60 TPSA 214.4	1 viol.	✓ Clean	`O=P(O)(O)O[C@@H]1[C@@H](O)[C@@H](O)[C@@H](OP(=O…`
ZINC100590871	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)O[C@H]1[C@H](O)[C@H](OP(=O)(O)O)[C@H](…`
ZINC1501016356	0.706	420.1 Da LogP -3.48 TPSA 261.0	1 viol.	✓ Clean	`O=P(O)(O)OC1C(O)[C@H](OP(=O)(O)O)C(O)[C@H](OP(=…`
ZINC31475423	0.703	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=O)…`
ZINC113539705	0.700	265.3 Da LogP 2.04 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(C#Cc2ccccc2)cc1)C(=O)O`
ZINC113539708	0.700	265.3 Da LogP 2.04 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(C#Cc2ccccc2)cc1)C(=O)O`
ZINC29566843	0.700	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1cccc(-c2ccccc2)c1)C(=O)O`
ZINC29570997	0.700	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(-c2ccccc2)c1)C(=O)O`
ZINC44283583	0.700	257.3 Da LogP 2.43 TPSA 72.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(Oc2ccccc2)cc1)C(=O)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.