NPASS Compound

Structure

CID57512 OpenBabel06191715392D 26 28 0 0 0 0 0 0 0 0999 V2000 0.5000 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1603 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4282 -6.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4282 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6962 -3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0981 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4282 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8301 -2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.2321 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.2942 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5622 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6028 -3.6103 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1 23 1 0 0 0 0 2 24 1 0 0 0 0 3 25 1 0 0 0 0 4 5 1 0 0 0 0 4 12 2 0 0 0 0 5 17 2 0 0 0 0 6 7 1 0 0 0 0 6 13 1 0 0 0 0 7 21 1 0 0 0 0 8 12 1 0 0 0 0 8 16 2 0 0 0 0 9 13 2 0 0 0 0 9 18 1 0 0 0 0 10 14 2 0 0 0 0 10 19 1 0 0 0 0 11 15 2 0 0 0 0 11 21 1 0 0 0 0 12 15 1 0 0 0 0 13 14 1 0 0 0 0 14 16 1 0 0 0 0 15 20 1 0 0 0 0 16 21 1 0 0 0 0 17 20 1 0 0 0 0 17 23 1 0 0 0 0 18 19 2 0 0 0 0 18 24 1 0 0 0 0 19 25 1 0 0 0 0 20 22 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	337.13
Volume:	345.316
LogP:	2.791
LogD:	2.795
LogS:	-4.662
# Rotatable Bonds:	3
TPSA:	49.69
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.736
Synthetic Accessibility Score:	2.497
Fsp3:	0.25
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.807
MDCK Permeability:	1.9685352526721545e-05
Pgp-inhibitor:	0.869
Pgp-substrate:	0.941
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.022
30% Bioavailability (F30%):	0.182

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.892
Plasma Protein Binding (PPB):	84.71464538574219%
Volume Distribution (VD):	1.237
Pgp-substrate:	5.359897613525391%

ADMET: Metabolism

CYP1A2-inhibitor:	0.524
CYP1A2-substrate:	0.964
CYP2C19-inhibitor:	0.759
CYP2C19-substrate:	0.373
CYP2C9-inhibitor:	0.77
CYP2C9-substrate:	0.91
CYP2D6-inhibitor:	0.023
CYP2D6-substrate:	0.941
CYP3A4-inhibitor:	0.661
CYP3A4-substrate:	0.601

ADMET: Excretion

Clearance (CL):	5.72
Half-life (T1/2):	0.426

ADMET: Toxicity

hERG Blockers:	0.185
Human Hepatotoxicity (H-HT):	0.209
Drug-inuced Liver Injury (DILI):	0.863
AMES Toxicity:	0.817
Rat Oral Acute Toxicity:	0.071
Maximum Recommended Daily Dose:	0.817
Skin Sensitization:	0.253
Carcinogencity:	0.558
Eye Corrosion:	0.003
Eye Irritation:	0.02
Respiratory Toxicity:	0.747

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC57512

Natural Product ID:	NPC57512
*Common Name:**	Palmatrubine
IUPAC Name:	2,3,10-trimethoxy-5,6-dihydroisoquinolino[2,1-b]isoquinolin-7-ium-9-ol;chloride
Synonyms:
Standard InCHIKey:	DFUDAUWKWTTXFV-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C20H19NO4.ClH/c1-23-17-5-4-12-8-16-14-10-19(25-3)18(24-2)9-13(14)6-7-21(16)11-15(12)20(17)22;/h4-5,8-11H,6-7H2,1-3H3;1H
SMILES:	COc1cc2c(cc1OC)CCn1c2cc2ccc(c(=O)c2c1)OC.Cl
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2270069
PubChem CID:	10547385
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0001909] Protoberberine alkaloids and derivatives

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO25734	Tinospora sagittata	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28836430]
NPO13757	Coptis japonica	Species	Ranunculaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21401114]
NPO10008	Tinospora capillipes	Species	Menispermaceae	Eukaryota	n.a.	root	n.a.	PMID[17340259]
NPO13757	Coptis japonica	Species	Ranunculaceae	Eukaryota	rhizomes	n.a.	n.a.	PMID[11000020]
NPO13757	Coptis japonica	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22622	Coptis deltoidea	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10008	Tinospora capillipes	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5649	Coptis chinensis	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29008	Coptis teeta	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25734	Tinospora sagittata	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
Others	12

Activity Type	# Activity
Organism	12

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Unit	Reference
NPT822	Organism	Lemna minor	Lemna minor	Activity	=	%	PMID[516131]
NPT823	Organism	Agrostis stolonifera var. palustris	Agrostis stolonifera var. palustris	Activity	=	%	PMID[516131]
NPT824	Organism	Ustilago maydis	Ustilago maydis	Inhibition	=	%	PMID[516131]
NPT825	Organism	Phytophthora infestans	Phytophthora infestans	Inhibition	=	%	PMID[516131]
NPT529	Organism	Rhizoctonia solani	Rhizoctonia solani	Inhibition	=	%	PMID[516131]
NPT826	Organism	Magnaporthe oryzae	Magnaporthe oryzae	Inhibition	=	%	PMID[516131]
NPT827	Organism	Mycosphaerella graminicola	Mycosphaerella graminicola	Inhibition	=	%	PMID[516131]
NPT828	Organism	Phaeosphaeria nodorum	Phaeosphaeria nodorum	Inhibition	=	%	PMID[516131]
NPT829	Organism	Puccinia recondita	Puccinia recondita	Activity	=	%	PMID[516131]
NPT825	Organism	Phytophthora infestans	Phytophthora infestans	Activity	=	%	PMID[516131]

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☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC57512 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	496
0.1-0.2	3487
0.2-0.3	12877
0.3-0.4	3552
0.4-0.5	14426
0.5-0.6	5824
0.6-0.7	1687
0.7-0.8	298
0.8-0.85	42
0.85-0.9	5
0.9-0.95	1
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
0.9795	High Similarity	NPC476580
0.9477	High Similarity	NPC306669
0.9286	High Similarity	NPC476569
0.9241	High Similarity	NPC4669
0.9073	High Similarity	NPC476579

Showing 1 to 5 of 200 entries

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Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC57512 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	305
0.1-0.2	725
0.2-0.3	932
0.3-0.4	1381
0.4-0.5	2755
0.5-0.6	2214
0.6-0.7	761
0.7-0.8	75
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8333	Intermediate Similarity	NPD3640	Phase 3
0.8333	Intermediate Similarity	NPD3639	Approved
0.8333	Intermediate Similarity	NPD3641	Approved
0.8289	Intermediate Similarity	NPD4664	Clinical (unspecified phase)
0.8101	Intermediate Similarity	NPD6031	Approved

Showing 1 to 5 of 200 entries

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Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data