NPASS Compound

Structure

CID210437 OpenBabel06191716002D 26 29 0 0 1 0 0 0 0 0999 V2000 -6.0622 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0 -6.0622 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 4.5000 0.0000 O 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 26 1 0 0 0 0 5 6 2 0 0 0 0 5 13 1 0 0 0 0 6 18 1 0 0 0 0 7 8 1 0 0 0 0 7 14 1 0 0 0 0 8 22 1 0 0 0 0 9 13 1 0 0 0 0 9 17 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 20 1 0 0 0 0 12 16 1 0 0 0 0 12 22 1 0 0 0 0 13 16 2 0 0 0 0 14 15 1 0 0 0 0 15 17 1 0 0 0 0 16 21 1 0 0 0 0 17 22 1 6 0 0 0 18 21 2 0 0 0 0 18 23 1 0 0 0 0 19 20 2 0 0 0 0 19 24 1 0 0 0 0 20 25 1 0 0 0 0 21 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	355.18
Volume:	367.885
LogP:	2.627
LogD:	3.025
LogS:	-2.674
# Rotatable Bonds:	4
TPSA:	40.16
# H-Bond Aceptor:	5
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.841
Synthetic Accessibility Score:	2.82
Fsp3:	0.429
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:	-5.131
MDCK Permeability:	2.739766932791099e-05
Pgp-inhibitor:	0.699
Pgp-substrate:	0.988
Human Intestinal Absorption (HIA):	0.003
20% Bioavailability (F20%):	0.198
30% Bioavailability (F30%):	0.323

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.984
Plasma Protein Binding (PPB):	71.91094970703125%
Volume Distribution (VD):	1.414
Pgp-substrate:	17.40007972717285%

ADMET: Metabolism

CYP1A2-inhibitor:	0.155
CYP1A2-substrate:	0.967
CYP2C19-inhibitor:	0.294
CYP2C19-substrate:	0.948
CYP2C9-inhibitor:	0.016
CYP2C9-substrate:	0.749
CYP2D6-inhibitor:	0.548
CYP2D6-substrate:	0.939
CYP3A4-inhibitor:	0.116
CYP3A4-substrate:	0.929

ADMET: Excretion

Clearance (CL):	11.606
Half-life (T1/2):	0.727

ADMET: Toxicity

hERG Blockers:	0.097
Human Hepatotoxicity (H-HT):	0.125
Drug-inuced Liver Injury (DILI):	0.784
AMES Toxicity:	0.076
Rat Oral Acute Toxicity:	0.655
Maximum Recommended Daily Dose:	0.962
Skin Sensitization:	0.202
Carcinogencity:	0.081
Eye Corrosion:	0.003
Eye Irritation:	0.017
Respiratory Toxicity:	0.955

Download Data

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

Natural Product: NPC210437

Natural Product ID:	NPC210437
*Common Name:**	Tetrahydropalmatine
IUPAC Name:	(13aS)-2,3,9,10-tetramethoxy-6,8,13,13a-tetrahydro-5H-isoquinolino[2,1-b]isoquinoline
Synonyms:	(-)-Tetrahydropalmatine; L-Tetrahydropalmatine; Tetrahydropalmatine
Standard InCHIKey:	AEQDJSLRWYMAQI-KRWDZBQOSA-N
Standard InCHI:	InChI=1S/C21H25NO4/c1-23-18-6-5-13-9-17-15-11-20(25-3)19(24-2)10-14(15)7-8-22(17)12-16(13)21(18)26-4/h5-6,10-11,17H,7-9,12H2,1-4H3/t17-/m0/s1
SMILES:	COc1ccc2C[C@H]3c4cc(c(cc4CCN3Cc2c1OC)OC)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL487182
PubChem CID:	72301
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
NPO22151	Stephania pierrei	Species	Menispermaceae	Eukaryota	tubers	n.a.	n.a.	PMID[8254346]
NPO827	Corydalis yanhusuo	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32058719]
NPO14045	Corydalis decumbens	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31599578]
NPO13962	Corydalis turtschaninovii	Species	Papaveraceae	Eukaryota	n.a.	tuber	n.a.	PMID[25670016]
NPO29471	Achyrocline satureioides	Species	Asteraceae	Eukaryota	aerial parts	Alpa Corral, Cordoba, Argentina	2008-Aug	PMID[25517209]
NPO13962	Corydalis turtschaninovii	Species	Papaveraceae	Eukaryota	n.a.	rhizome	n.a.	PMID[25277281]
NPO827	Corydalis yanhusuo	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23194502]
NPO827	Corydalis yanhusuo	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22737858]
NPO13757	Coptis japonica	Species	Ranunculaceae	Eukaryota	n.a.	rhizome	n.a.	PMID[21401114]
NPO25345	Corydalis ternata	Species	Papaveraceae	Eukaryota	tubers	n.a.	n.a.	PMID[20594848]

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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
ED50	2
IC50	5
Ki	8
Others	18

Activity Type	# Activity
Individual Protein	24
Organism	7
Others	1
SINGLE PROTEIN	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	0.09	%	PMID[486811]
NPT20556	SINGLE PROTEIN	Replicase polyprotein 1ab	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	7.96	%	PMID[486810]
NPT242	Individual Protein	Dopamine D1 receptor	Homo sapiens	IC50	=	1630.0	nM	PMID[486809]
NPT243	Individual Protein	Dopamine D2 receptor	Homo sapiens	IC50	=	450.0	nM	PMID[486809]
NPT242	Individual Protein	Dopamine D1 receptor	Homo sapiens	Activity	=	-7.43	%	PMID[486809]
NPT243	Individual Protein	Dopamine D2 receptor	Homo sapiens	Activity	=	3.51	%	PMID[486809]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Hit score	=	0.0185	n.a.	PMID[486808]
NPT20555	ORGANISM	SARS-CoV-2	Severe acute respiratory syndrome coronavirus 2	Inhibition	=	-11.62	%	PMID[486807]
NPT242	Individual Protein	Dopamine D1 receptor	Homo sapiens	Ki	=	153.0	nM	PMID[486806]
NPT243	Individual Protein	Dopamine D2 receptor	Homo sapiens	Ki	=	1125.0	nM	PMID[486806]

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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 NPC210437 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	326
0.1-0.2	1697
0.2-0.3	9832
0.3-0.4	7996
0.4-0.5	6608
0.5-0.6	11864
0.6-0.7	3415
0.7-0.8	505
0.8-0.85	263
0.85-0.9	130
0.9-0.95	48
0.95-1	13

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC106295
1.0	High Similarity	NPC51957
1.0	High Similarity	NPC476144
1.0	High Similarity	NPC16107
0.9928	High Similarity	NPC7467

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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 NPC210437 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	205
0.1-0.2	762
0.2-0.3	1055
0.3-0.4	1702
0.4-0.5	2684
0.5-0.6	1804
0.6-0.7	699
0.7-0.8	203
0.8-0.85	25
0.85-0.9	9
0.9-0.95	0
0.95-1	2

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD4584	Approved
0.9565	High Similarity	NPD4664	Clinical (unspecified phase)
0.8993	High Similarity	NPD7298	Approved
0.8792	High Similarity	NPD4017	Approved
0.879	High Similarity	NPD8099	Discontinued

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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