NPASS Compound

Structure

NPC482767 OpenBabel06302215092D 43 44 0 0 1 0 0 0 0 0999 V2000 11.0878 3.5211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5878 4.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5878 4.3871 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0878 3.5211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0878 3.5211 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5878 2.6551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5878 2.6551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0878 1.7891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0878 1.7891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5878 0.9230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5878 0.9230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0878 0.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0878 0.0570 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5878 -0.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5878 -0.8090 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -1.6180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 -1.3090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9511 -0.3090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7601 0.2788 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6555 1.2733 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4646 1.8611 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3781 1.4543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4826 0.4598 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3962 0.0531 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2052 0.6409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1187 0.2341 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2233 -0.7604 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1368 -1.1671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2413 -2.1617 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1549 -2.5684 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -8.3628 -3.5465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.3573 -3.6511 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -9.8573 -4.5171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.8573 -4.5171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.3573 -3.6511 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.3573 -5.3831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.7641 -2.7375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.7422 -2.5296 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.0209 -2.0684 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5007 -0.9414 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6736 -0.1280 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0878 -1.6750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 43 1 1 0 0 0 15 14 1 1 0 0 0 15 16 1 0 0 0 0 15 42 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 18 42 1 0 0 0 0 19 20 1 0 0 0 0 19 41 1 6 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 24 40 1 6 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 29 30 1 0 0 0 0 30 39 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 0 0 0 0 32 33 1 0 0 0 0 32 37 1 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 34 36 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	610.48
Volume:	670.358
LogP:	7.116
LogD:	4.412
LogS:	-6.53
# Rotatable Bonds:	27
TPSA:	113.29
# H-Bond Aceptor:	7
# H-Bond Donor:	3
# Rings:	2
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.064
Synthetic Accessibility Score:	4.577
Fsp3:	0.944
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.024
MDCK Permeability:	8.722547136130743e-06
Pgp-inhibitor:	0.01
Pgp-substrate:	0.982
Human Intestinal Absorption (HIA):	0.022
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	97.94011688232422%
Volume Distribution (VD):	0.974
Pgp-substrate:	2.272191047668457%

ADMET: Metabolism

CYP1A2-inhibitor:	0.013
CYP1A2-substrate:	0.247
CYP2C19-inhibitor:	0.065
CYP2C19-substrate:	0.048
CYP2C9-inhibitor:	0.073
CYP2C9-substrate:	0.98
CYP2D6-inhibitor:	0.002
CYP2D6-substrate:	0.063
CYP3A4-inhibitor:	0.285
CYP3A4-substrate:	0.031

ADMET: Excretion

Clearance (CL):	4.999
Half-life (T1/2):	0.093

ADMET: Toxicity

hERG Blockers:	0.62
Human Hepatotoxicity (H-HT):	0.801
Drug-inuced Liver Injury (DILI):	0.182
AMES Toxicity:	0.005
Rat Oral Acute Toxicity:	0.002
Maximum Recommended Daily Dose:	0.813
Skin Sensitization:	0.981
Carcinogencity:	0.037
Eye Corrosion:	0.005
Eye Irritation:	0.179
Respiratory Toxicity:	0.77

Download Data

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

Natural Product: NPC482767

Natural Product ID:	NPC482767
*Common Name:**	XDRCAAHFKMXOBD-JMDUBUIHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XDRCAAHFKMXOBD-JMDUBUIHSA-N
Standard InCHI:	InChI=1S/C36H66O7/c1-3-4-5-6-7-8-9-10-11-12-16-22-32(39)34-24-25-35(43-34)33(40)23-18-17-20-30(38)19-14-13-15-21-31-27-29(26-28(2)37)36(41)42-31/h29-35,38-40H,3-27H2,1-2H3/t29?,30-,31?,32-,33-,34-,35-/m1/s1
SMILES:	CCCCCCCCCCCCC[C@H]([C@H]1CC[C@H]([C@@H](CCCC[C@@H](CCCCCC2CC(CC(=O)C)C(=O)O2)O)O)O1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	44559004
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001334] Fatty alcohols [CHEMONTID:0002518] Annonaceous acetogenins

*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
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	bark	n.a.	PMID[1479382]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	bark	n.a.	n.a.	PMID[1479382]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1791471]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2614426]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9322367]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9917277]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO7202	Goniothalamus giganteus	Species	Annonaceae	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

Activity Type	# Activity
ED50	6
Others	2

Activity Type	# Activity
Cell Line	6
Organism	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	ED50	=	1.4	10'-2 ug/ml	PMID[9917277]
NPT83	Cell Line	MCF7	Homo sapiens	ED50	=	7.6	10'-4 ug/ml	PMID[9917277]
NPT139	Cell Line	HT-29	Homo sapiens	ED50	=	7.4	10'-4 ug/ml	PMID[9917277]
NPT376	Cell Line	A498	Homo sapiens	ED50	=	1.2	10'-1 ug/ml	PMID[9917277]
NPT306	Cell Line	PC-3	Homo sapiens	ED50	=	5.7	10'-2 ug/ml	PMID[9917277]
NPT783	Cell Line	MIA PaCa-2	Homo sapiens	ED50	=	7.4	10'-2 ug/ml	PMID[9917277]
NPT140	Organism	Artemia	Artemia	LC50	=	0.4	ug.mL-1	PMID[9917277]
NPT1381	Organism	Aedes aegypti	Aedes aegypti	LC50	=	54.2	ug.mL-1	PMID[9917277]

☑ 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 NPC482767 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	477
0.1-0.2	3885
0.2-0.3	12649
0.3-0.4	12257
0.4-0.5	8544
0.5-0.6	4160
0.6-0.7	656
0.7-0.8	44
0.8-0.85	6
0.85-0.9	1
0.9-0.95	7
0.95-1	11

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 NPC482767 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	655
0.1-0.2	3959
0.2-0.3	3009
0.3-0.4	890
0.4-0.5	466
0.5-0.6	154
0.6-0.7	16
0.7-0.8	1
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
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