NPASS Compound

Structure

NPC66436 OpenBabel06302215192D 27 29 0 0 1 0 0 0 0 0999 V2000 1.0934 1.6637 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8366 0.9945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8147 1.2024 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2215 2.1160 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3147 0.3364 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3092 0.2319 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8970 1.0409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8916 0.9364 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2983 0.0228 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7105 -0.7862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7160 -0.6817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1172 -1.6997 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5295 -2.5088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2928 -0.0817 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4793 1.7454 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4739 1.6409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6456 -0.4067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 1 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 0.8660 -1.5000 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 -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 -1.7321 -0.0000 0.0000 O 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 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 18 1 0 0 0 0 3 4 1 1 0 0 0 3 5 1 0 0 0 0 5 6 1 1 0 0 0 5 17 1 0 0 0 0 6 11 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 15 1 0 0 0 0 9 10 2 0 0 0 0 9 14 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 15 16 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 1 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 27 1 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	374.17
Volume:	383.025
LogP:	3.867
LogD:	3.503
LogS:	-4.687
# Rotatable Bonds:	5
TPSA:	77.38
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.816
Synthetic Accessibility Score:	3.488
Fsp3:	0.429
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.741
MDCK Permeability:	2.095543641189579e-05
Pgp-inhibitor:	0.106
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	0.26

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.028
Plasma Protein Binding (PPB):	90.30455780029297%
Volume Distribution (VD):	0.594
Pgp-substrate:	10.088663101196289%

ADMET: Metabolism

CYP1A2-inhibitor:	0.061
CYP1A2-substrate:	0.959
CYP2C19-inhibitor:	0.381
CYP2C19-substrate:	0.862
CYP2C9-inhibitor:	0.806
CYP2C9-substrate:	0.893
CYP2D6-inhibitor:	0.234
CYP2D6-substrate:	0.88
CYP3A4-inhibitor:	0.642
CYP3A4-substrate:	0.724

ADMET: Excretion

Clearance (CL):	10.447
Half-life (T1/2):	0.642

ADMET: Toxicity

hERG Blockers:	0.096
Human Hepatotoxicity (H-HT):	0.155
Drug-inuced Liver Injury (DILI):	0.732
AMES Toxicity:	0.1
Rat Oral Acute Toxicity:	0.118
Maximum Recommended Daily Dose:	0.122
Skin Sensitization:	0.887
Carcinogencity:	0.06
Eye Corrosion:	0.005
Eye Irritation:	0.603
Respiratory Toxicity:	0.654

Download Data

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

Natural Product: NPC66436

Natural Product ID:	NPC66436
*Common Name:**	KBIHHHDCLJQNHG-QRSJPUFVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KBIHHHDCLJQNHG-QRSJPUFVSA-N
Standard InCHI:	InChI=1S/C21H26O6/c1-11-12(2)21(14-9-17(25-4)19(23)18(10-14)26-5)27-20(11)13-6-7-15(22)16(8-13)24-3/h6-12,20-23H,1-5H3/t11-,12+,20+,21-/m0/s1
SMILES:	C[C@H]1[C@@H](C)[C@@H](c2cc(c(c(c2)OC)O)OC)O[C@H]1c1ccc(c(c1)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans [CHEMONTID:0001604] Tetrahydrofuran lignans [CHEMONTID:0003423] 7,7'-epoxylignans

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	seeds	n.a.	n.a.	PMID[17998162]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1955885]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	n.a.	fruit	n.a.	PMID[20879744]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27419473]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	Aril	n.a.	n.a.	Database[FooDB]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	Leaf Essent. Oil	n.a.	n.a.	Database[FooDB]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO8303	Catalpa bignonioides	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1382	Hyptis tomentosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO8303	Catalpa bignonioides	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1382	Hyptis tomentosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1382	Hyptis tomentosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Title]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO6113	Piper pedicellosum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5162	Comaster multifida	Species	Comatulidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4539	Ipomoea cristulata	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO490	Lophozonia menziesii	Species	0thofagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17811	Cephalonoplos segetum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5746	Pancratium trianthum	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5241	Myristica fragrans	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7393	Esenbeckia nesiotica	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19928	Lachnoanaerobaculum saburreum	Species	Lachnospiraceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5334	Rhodotypos scandens	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7237	Xanthostemon oppositifolius	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2665	Andinobates fulguritus	Species	Dendrobatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8303	Catalpa bignonioides	Species	Bignoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28409	Lens phaseoloides	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8532	Helipterum tenellum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1382	Hyptis tomentosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ 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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC66436 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	393
0.1-0.2	1323
0.2-0.3	3619
0.3-0.4	10352
0.4-0.5	8634
0.5-0.6	4309
0.6-0.7	8048
0.7-0.8	4310
0.8-0.85	889
0.85-0.9	596
0.9-0.95	184
0.95-1	40

Similarity Score	Similarity Level	Natural Product ID

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 NPC66436 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	317
0.1-0.2	790
0.2-0.3	1764
0.3-0.4	2749
0.4-0.5	1751
0.5-0.6	1027
0.6-0.7	609
0.7-0.8	129
0.8-0.85	11
0.85-0.9	2
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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