Protein profile

PA1815

ribonuclease HI

Genome: NC_002516.2

Gene: rnhA PA1815 Structure source: AlphaFold UniProt Q9I2S9

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Amino acids 148

Annotations 6

Features 14

PDB binders 1

Druggability 0.48

Overview

Basic information about this protein and its source genome.

Accession: PA1815
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: rnhA PA1815
Status: annotated
Amino acids: 148
Structure source: AlphaFold

3.1.26.4

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0000287 Binding to a magnesium (Mg) ion. GO:0003676 Binding to a nucleic acid. GO:0004523 Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters. GO:0043137 Removal of the Okazaki RNA primer from the lagging strand of replicating DNA, by a combination of the actions of DNA polymerase, DNA helicase and an endonuclease.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 36.806
Human E-value: 5.59e-20
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Unknown

Selected Druggability evidence

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 0.48

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

3.1.26.4

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0003676 Binding to a nucleic acid.
GO:0004523 Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
GO:0043137 Removal of the Okazaki RNA primer from the lagging strand of replicating DNA, by a combination of the actions of DNA polymerase, DNA helicase and an endonuclease.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
6	142	CDD	cd09278	RNase_HI_prokaryote_like
6	142	InterPro	IPR022892	Ribonuclease HI
4	148	Hamap	MF_00042	Ribonuclease H [rnhA].
4	148	InterPro	IPR022892	Ribonuclease HI
1	146	FunFam	G3DSA:3.30.420.10:FF:000119	Ribonuclease H
3	144	ProSiteProfiles	PS50879	RNase H type-1 domain profile.
3	144	InterPro	IPR002156	Ribonuclease H domain
3	143	PANTHER	PTHR10642	RIBONUCLEASE H1
5	143	SUPERFAMILY	SSF53098	Ribonuclease H-like
5	143	InterPro	IPR012337	Ribonuclease H-like superfamily
5	143	Pfam	PF00075	RNase H
5	143	InterPro	IPR002156	Ribonuclease H domain
1	146	Gene3D	G3DSA:3.30.420.10	-
1	146	InterPro	IPR036397	Ribonuclease H superfamily

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
AlphaFold PA1815	AlphaFold	—	—	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
2				0.48

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
FLC	2QK9	O60930	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL562080	O60930	6.77	415.7 Da LogP 3.81 TPSA 103.5	✓ Ro5	✓ Clean	`O=C(O)c1nc(Cc2c(Br)sc3ccc(Cl)cc23)nc(O)c1O`
JTH	O60930	6.22	180.2 Da LogP 1.58 TPSA 57.5	✓ Ro5	✓ Clean	`CC(C)C1=CC=C(C(=O)C(=C1)O)O`
P1Y	O60930	6.05	355.1 Da LogP 1.95 TPSA 112.8	✓ Ro5	✓ Clean	`COc1ccc(cc1Br)Cc2nc(c(c(n2)O)O)C(=O)O`
CHEMBL124363	Q06347	—	248.2 Da LogP -0.71 TPSA 84.3	✓ Ro5	✓ Clean	`C#C[C@@]1(CO)C=C[C@H](n2cc(C)c(=O)[nH]c2=O)O1`
CHEMBL210651	Q06347	—	229.3 Da LogP -0.59 TPSA 90.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2CO[C@@H](CO)S2)c(=O)n1`
CHEMBL515564	Q06347	—	569.7 Da LogP 6.86 TPSA 134.6	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCCOCCCOP(=O)(O)CO[C@H](C)Cn1cnc2c…`
CHEMBL519846	Q06347	—	286.2 Da LogP -0.95 TPSA 159.4	✓ Ro5	Alert	`[N-]=[N+]=N[C@]1(CO)O[C@@H](n2ccc(N)nc2=O)[C@@H…`

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
ZINC146345594	1.000	286.2 Da LogP -0.95 TPSA 159.4	✓ Ro5	Alert	`[N-]=[N+]=N[C@]1(CO)O[C@@H](n2ccc(N)nc2=O)[C@@H…`
ZINC3779991	1.000	229.3 Da LogP -0.59 TPSA 90.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2CO[C@@H](CO)S2)c(=O)n1`
ZINC3819454	1.000	248.2 Da LogP -0.71 TPSA 84.3	✓ Ro5	✓ Clean	`C#C[C@@]1(CO)C=C[C@H](n2cc(C)c(=O)[nH]c2=O)O1`
ZINC40940341	1.000	286.2 Da LogP -0.95 TPSA 159.4	✓ Ro5	Alert	`[N-]=[N+]=N[C@]1(CO)O[C@@H](n2ccc(N)nc2=O)[C@@H…`
ZINC66031969	1.000	248.2 Da LogP -0.71 TPSA 84.3	✓ Ro5	✓ Clean	`C#C[C@]1(CO)C=C[C@@H](n2cc(C)c(=O)[nH]c2=O)O1`
ZINC13973993	0.808	284.2 Da LogP -1.92 TPSA 179.6	✓ Ro5	Alert	`[N-]=[N+]=N[C@]1(CO)O[C@@H](n2ccc(N)nc2=O)[C@H]…`
ZINC142707132	0.808	284.2 Da LogP -1.92 TPSA 179.6	✓ Ro5	Alert	`[N-]=[N+]=N[C@]1(CO)O[C@@H](n2ccc(N)nc2=O)[C@@H…`
ZINC34987189	0.808	284.2 Da LogP -1.92 TPSA 179.6	✓ Ro5	Alert	`[N-]=[N+]=N[C@]1(CO)O[C@H](n2ccc(N)nc2=O)[C@H](…`
ZINC38424636	0.808	284.2 Da LogP -1.92 TPSA 179.6	✓ Ro5	Alert	`[N-]=[N+]=N[C@]1(CO)O[C@H](n2ccc(N)nc2=O)[C@@H]…`
ZINC38424637	0.808	284.2 Da LogP -1.92 TPSA 179.6	✓ Ro5	Alert	`[N-]=[N+]=N[C@]1(CO)O[C@@H](n2ccc(N)nc2=O)[C@@H…`
ZINC40834027	0.796	286.2 Da LogP -0.95 TPSA 159.4	✓ Ro5	Alert	`[N-]=[N+]=N[C@]1(CO)O[C@@H](n2ccc(N)nc2=O)[C@H]…`
ZINC77271410	0.733	315.3 Da LogP 0.99 TPSA 125.4	✓ Ro5	✓ Clean	`CCO[P@](=O)(O)CO[C@H](C)Cn1cnc2c(N)ncnc21`
ZINC85210532	0.733	315.3 Da LogP 0.99 TPSA 125.4	✓ Ro5	✓ Clean	`CCO[P@](=O)(O)CO[C@@H](C)Cn1cnc2c(N)ncnc21`
ZINC1543475	0.650	287.2 Da LogP -0.05 TPSA 136.4	✓ Ro5	✓ Clean	`C[C@H](Cn1cnc2c(N)ncnc21)OCP(=O)(O)O`
ZINC2020246	0.650	287.2 Da LogP -0.05 TPSA 136.4	✓ Ro5	✓ Clean	`C[C@@H](Cn1cnc2c(N)ncnc21)OCP(=O)(O)O`
ZINC13516370	0.641	447.2 Da LogP 0.18 TPSA 229.4	1 viol.	✓ Clean	`C[C@H](Cn1cnc2c(N)ncnc21)OC[P@@](=O)(O)O[P@@](=…`
ZINC2382415324	0.638	286.2 Da LogP -0.71 TPSA 160.3	✓ Ro5	Alert	`[N-]=[N+]=N[C@]1(CO)O[C@@H](n2ccc(=N)nc2O)[C@H]…`
ZINC12346	0.625	229.3 Da LogP -0.59 TPSA 90.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2CS[C@H](CO)O2)c(=O)n1`
ZINC1616230	0.625	229.3 Da LogP -0.59 TPSA 90.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2CS[C@H](CO)O2)c(=O)n1`
ZINC16952920	0.625	229.3 Da LogP -0.59 TPSA 90.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2CS[C@@H](CO)O2)c(=O)n1`
ZINC17187710	0.625	229.3 Da LogP -0.59 TPSA 90.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2CS[C@@H](CO)O2)c(=O)n1`
ZINC202529174	0.621	363.3 Da LogP 2.04 TPSA 125.4	✓ Ro5	✓ Clean	`C[C@H](Cn1cnc2c(N)ncnc21)OC[P@@](=O)(O)Oc1ccccc1`
ZINC208827522	0.621	363.3 Da LogP 2.04 TPSA 125.4	✓ Ro5	✓ Clean	`C[C@@H](Cn1cnc2c(N)ncnc21)OC[P@@](=O)(O)Oc1cccc…`
ZINC146973421	0.614	293.7 Da LogP -0.98 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@](CO)(CCl)[C@@H](O)[C@H]2F)c…`
ZINC104233784	0.594	377.5 Da LogP 3.71 TPSA 99.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOC[C@H](O)Cn1cnc2c(N)ncnc21`
ZINC104233791	0.594	377.5 Da LogP 3.71 TPSA 99.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOC[C@@H](O)Cn1cnc2c(N)ncnc21`
ZINC1642844	0.583	213.2 Da LogP -1.31 TPSA 99.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2CO[C@H](CO)O2)c(=O)n1`
ZINC1642845	0.583	213.2 Da LogP -1.31 TPSA 99.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2CO[C@H](CO)O2)c(=O)n1`
ZINC29412715	0.583	230.2 Da LogP -0.88 TPSA 84.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2CO[C@@H](CO)S2)c(=O)[nH]1`
ZINC3779994	0.583	230.2 Da LogP -0.88 TPSA 84.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2CO[C@@H](CO)S2)c(=O)[nH]1`
ZINC35328439	0.567	494.5 Da LogP 1.70 TPSA 197.8	1 viol.	Alert	`CC(C)C(=O)OC[C@@]1(N=[N+]=[N-])O[C@@H](n2ccc(N)…`
ZINC59026194	0.567	267.2 Da LogP -1.11 TPSA 142.6	✓ Ro5	Alert	`[N-]=[N+]=N[C@]1(CO)O[C@@H]2[C@@H](Oc3nc(=O)ccn…`
ZINC206737780	0.565	358.3 Da LogP 0.02 TPSA 165.5	✓ Ro5	✓ Clean	`C[C@H](N[P@@](=O)(O)CO[C@H](C)Cn1cnc2c(N)ncnc21…`
ZINC142218533	0.559	422.4 Da LogP 1.76 TPSA 171.5	✓ Ro5	Alert	`CC(C)C(=O)OC[C@@]1(N=[N+]=[N-])O[C@@H](n2ccc(N)…`
ZINC6524890	0.554	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](F)[C@H]2O)c(=O)n1`
ZINC85475812	0.554	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](F)[C@H]2O)c(=O)n1`
ZINC11949639	0.552	215.1 Da LogP 3.28 TPSA 20.2	✓ Ro5	✓ Clean	`CC(C)c1ccc(O)c(Br)c1`
ZINC95709551	0.552	262.1 Da LogP 3.12 TPSA 20.2	✓ Ro5	✓ Clean	`CC(C)c1ccc(I)c(O)c1`
ZINC514286885	0.549	400.4 Da LogP 0.89 TPSA 154.5	✓ Ro5	✓ Clean	`CC(C)OC(=O)[C@H](C)N[P@](=O)(O)CO[C@H](C)Cn1cnc…`
ZINC13546396	0.544	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2F)c(=O)n1`
ZINC16952044	0.544	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@H]2F)c(=O)n1`
ZINC17174505	0.544	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2F)c(=O…`
ZINC17174506	0.544	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2F)c(=O)…`
ZINC2522524	0.544	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@@H]2F)c(=O)n1`
ZINC3817231	0.544	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2F)c(=O)n1`
ZINC57331	0.544	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2F)c(=O)…`
ZINC5758597	0.544	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2F)c(=O)n1`
ZINC5758598	0.544	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2F)c(=O)…`
ZINC59201305	0.544	245.2 Da LogP -1.59 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2F)c(=O)n1`
ZINC219787485	0.536	439.4 Da LogP 4.12 TPSA 114.4	✓ Ro5	✓ Clean	`C[C@@H](Cn1cnc2c(N)ncnc21)OCP(=O)(Oc1ccccc1)Oc1…`

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.