Properties – NPI Modulators Database

Targets: 77
Compounds: 199
Source PDB structures: 379
Binding sites: 636
Structure pairs: 3,051
Unique reference PDBs: 572

Compounds

Compound classes

n = 199

Molecular weight (Da)

n = 199

cLogP

n = 199

Topological polar surface area (Å²)

n = 199

Quantitative estimate of drug-likeness

n = 199

H-bond donors

n = 199

H-bond acceptors

n = 199

Rotatable bonds

n = 199

Targets

Protein Class Distribution in NPIMDB

Broad functional classification of 77 NPI-associated proteins based on InterPro family/domain annotations and manual curation.

Broad protein class	Count	Percentage
RNA-binding / RNA metabolism protein	17	22.1%
Nuclease / DNA-RNA repair enzyme	13	16.9%
DNA/RNA polymerase and replication protein	11	14.3%
Viral replication / viral nucleic-acid-related protein	7	9.1%
tRNA-related enzyme	6	7.8%
Other enzyme / miscellaneous	6	7.8%
Transcription factor / transcription regulator	5	6.5%
Translation / ribosomal protein	5	6.5%
DNA/RNA modification or nucleotide metabolism enzyme	4	5.2%
CRISPR-Cas / prokaryotic antiviral defense protein	2	2.6%
Argonaute / RNAi-related protein	1	1.3%
Total	77	100%

Source organisms

Target counts grouped by organism name

Compounds per target

Distinct compounds per target

Binding sites

Pocket properties count each source pocket once per UniProt accession.

Number of pocket residues

n = 636

2–4 7
4–6 36
6–8 73
8–10 91
10–12 70
12–14 112
14–16 192
16–18 19
18–20 16
20–22 11
22–24 4
24–26 5

Hydrophobic residues (%)

n = 636

0–10 30
10–20 48
20–30 110
30–40 104
40–50 241
50–60 69
60–70 16
70–80 11
80–90 5
90–100 2

Positively charged residues (%)

n = 636

0–10 66
10–20 98
20–30 121
30–40 290
40–50 36
50–60 15
60–70 8
70–80 2
80–90 0
90–100 0

Comparison with nucleic acid-bound reference structures

RMSD values come from the dataset’s protein structure alignments. Each comparison between a small molecule-bound structure and a reference structure contributes one record. A pocket can contribute multiple comparisons.

Reference structure binding states

572 unique reference PDBs

Pocket RMSD (Å)

n = 3,051

0–2 2,746
2–4 213
4–6 20
6–8 6
8–10 0
10–12 0
12–14 6
14–16 11
16–18 0
18–20 43
20–22 6

Global RMSD (Å)

n = 3,051

0–2 1,630
2–4 1,169
4–6 84
6–8 39
8–10 40
10–12 16
12–14 5
14–16 1
16–18 0
18–20 44
20–22 6
22–24 17

Pocket RMSD (Å)

n = 207

0–2 198
2–4 2
4–6 1
6–8 0
8–10 0
10–12 0
12–14 0
14–16 0
16–18 0
18–20 4
20–22 2

Global RMSD (Å)

n = 207

0–2 29
2–4 148
4–6 22
6–8 2
8–10 0
10–12 0
12–14 0
14–16 0
16–18 0
18–20 5
20–22 1
22–24 0

Pocket RMSD (Å)

n = 1,314

0–2 1,111
2–4 126
4–6 17
6–8 0
8–10 0
10–12 0
12–14 6
14–16 11
16–18 0
18–20 39
20–22 4

Global RMSD (Å)

n = 1,314

0–2 836
2–4 342
4–6 45
6–8 8
8–10 15
10–12 1
12–14 5
14–16 1
16–18 0
18–20 39
20–22 5
22–24 17

Pocket RMSD (Å)

n = 1,530

0–2 1,437
2–4 85
4–6 2
6–8 6
8–10 0
10–12 0
12–14 0
14–16 0
16–18 0
18–20 0
20–22 0

Global RMSD (Å)

n = 1,530

0–2 765
2–4 679
4–6 17
6–8 29
8–10 25
10–12 15
12–14 0
14–16 0
16–18 0
18–20 0
20–22 0
22–24 0

Compounds

Compound classes

Molecular weight (Da)

cLogP

Topological polar surface area (Å²)

Quantitative estimate of drug-likeness

H-bond donors

H-bond acceptors

Rotatable bonds

Molecular weight (Da)

cLogP

Topological polar surface area (Å²)

Quantitative estimate of drug-likeness

H-bond donors

H-bond acceptors

Rotatable bonds

Molecular weight (Da)

cLogP

Topological polar surface area (Å²)

Quantitative estimate of drug-likeness

H-bond donors

H-bond acceptors

Rotatable bonds

Molecular weight (Da)

cLogP

Topological polar surface area (Å²)

Quantitative estimate of drug-likeness

H-bond donors

H-bond acceptors

Rotatable bonds

Targets

Protein Class Distribution in NPIMDB

Source organisms

Compounds per target

Binding sites

Number of pocket residues ! Count of distinct standard amino acid residues in the source biological assembly with at least one atom within the distance cutoff of any atom of the selected compound instance. Cutoff in this dataset: 4 Å.

Hydrophobic residues (%) ! Percentage of source pocket residues classified as hydrophobic in NPIMDB: Ala, Val, Ile, Leu, Met, Phe, Trp and Pro.

Positively charged residues (%) ! Percentage of source pocket residues classified as positively charged in NPIMDB: Arg, Lys and His. This uses residue identity.

Comparison with nucleic acid-bound reference structures

Reference structure binding states

Pocket RMSD (Å)

Global RMSD (Å)

Pocket RMSD (Å)

Global RMSD (Å)

Pocket RMSD (Å)

Global RMSD (Å)

Pocket RMSD (Å)

Global RMSD (Å)

Global versus pocket RMSD

Number of pocket residues

Hydrophobic residues (%)

Positively charged residues (%)