NPASS Compound

Structure

NPC481746 OpenBabel06302216152D 49 52 0 0 1 0 0 0 0 0999 V2000 6.0622 11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 12.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 11.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 10.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 6.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 5.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 4.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2459 4.6235 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.2209 4.4010 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.3699 5.3898 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3008 5.7551 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.6547 3.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.2209 2.5990 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2459 2.3765 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.1563 1.3805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0758 0.9875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2983 0.0126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7338 1.7406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7297 1.6509 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 C 0 0 2 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 1.7321 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7321 4.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7321 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2321 3.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2321 4.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2321 4.8660 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 2.5000 0.0000 O 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 1.7321 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 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 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 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 4.0274 3.8262 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3753 3.5870 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.6547 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1517 4.7663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0234 5.5984 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 2 0 0 0 0 7 8 1 0 0 0 0 8 9 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 10 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 13 31 1 0 0 0 0 14 15 1 0 0 0 0 14 27 1 0 0 0 0 15 16 1 0 0 0 0 15 49 1 0 0 0 0 16 17 1 0 0 0 0 16 19 1 0 0 0 0 16 48 1 6 0 0 0 17 18 1 0 0 0 0 19 20 1 0 0 0 0 19 47 1 1 0 0 0 20 25 1 0 0 0 0 20 21 1 0 0 0 0 20 46 1 1 0 0 0 21 22 1 1 0 0 0 21 27 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 23 25 1 0 0 0 0 25 26 2 0 0 0 0 27 28 1 0 0 0 0 27 45 1 0 0 0 0 28 29 1 0 0 0 0 28 30 1 0 0 0 0 30 31 1 0 0 0 0 30 36 1 0 0 0 0 31 32 1 0 0 0 0 31 35 1 0 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 36 37 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 39 44 2 0 0 0 0 39 40 1 0 0 0 0 40 41 2 0 0 0 0 41 42 1 0 0 0 0 42 43 2 0 0 0 0 43 44 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	684.31
Volume:	693.4
LogP:	4.17
LogD:	1.748
LogS:	-3.775
# Rotatable Bonds:	13
TPSA:	211.28
# H-Bond Aceptor:	12
# H-Bond Donor:	7
# Rings:	4
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.058
Synthetic Accessibility Score:	5.599
Fsp3:	0.541
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:	-5.46
MDCK Permeability:	1.7189220670843497e-05
Pgp-inhibitor:	0.309
Pgp-substrate:	0.384
Human Intestinal Absorption (HIA):	0.855
20% Bioavailability (F20%):	0.672
30% Bioavailability (F30%):	0.962

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.077
Plasma Protein Binding (PPB):	92.2860107421875%
Volume Distribution (VD):	1.121
Pgp-substrate:	4.710392475128174%

ADMET: Metabolism

CYP1A2-inhibitor:	0.07
CYP1A2-substrate:	0.131
CYP2C19-inhibitor:	0.036
CYP2C19-substrate:	0.103
CYP2C9-inhibitor:	0.423
CYP2C9-substrate:	0.07
CYP2D6-inhibitor:	0.006
CYP2D6-substrate:	0.074
CYP3A4-inhibitor:	0.338
CYP3A4-substrate:	0.132

ADMET: Excretion

Clearance (CL):	1.83
Half-life (T1/2):	0.11

ADMET: Toxicity

hERG Blockers:	0.436
Human Hepatotoxicity (H-HT):	0.833
Drug-inuced Liver Injury (DILI):	0.033
AMES Toxicity:	0.009
Rat Oral Acute Toxicity:	0.204
Maximum Recommended Daily Dose:	0.943
Skin Sensitization:	0.624
Carcinogencity:	0.028
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.963

Download Data

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

Natural Product: NPC481746

Natural Product ID:	NPC481746
*Common Name:**	KIYRAHQQRCRVFP-IUIARIAISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KIYRAHQQRCRVFP-IUIARIAISA-N
Standard InCHI:	InChI=1S/C37H48O12/c1-6-7-8-9-10-11-15-18-26(39)48-31-27-29(41)34(44,20-38)33(43)37(47)25(19-22(4)28(37)40)36(27,46)23(5)30(35(31,45)21(2)3)49-32(42)24-16-13-12-14-17-24/h10-19,23,25,27,29-31,33,38,41,43-47H,2,6-9,20H2,1,3-5H3/b11-10+,18-15+/t23-,25+,27+,29+,30-,31-,33-,34+,35+,36+,37-/m1/s1
SMILES:	CCCCC/C=C/C=C/C(=O)O[C@@H]1[C@@H]2[C@@H]([C@@](CO)([C@H]([C@]3([C@@H](C=C(C)C3=O)[C@]2([C@H](C)[C@H]([C@]1(C(=C)C)O)OC(=O)c1ccccc1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds]

*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
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	flower	n.a.	PMID[21916433]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[23558238]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27228307]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31150241]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31860304]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32223193]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	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
IC50	3

Activity Type	# Activity
Cell Line	3

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT323	Cell Line	SW-620	Homo sapiens	IC50	>	10000.0	nM	PMID[32223193]
NPT2170	Cell Line	RKO	Homo sapiens	IC50	>	10000.0	nM	PMID[32223193]
NPT114	Cell Line	LoVo	Homo sapiens	IC50	>	10000.0	nM	PMID[32223193]

☑ 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 NPC481746 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	321
0.1-0.2	1129
0.2-0.3	2402
0.3-0.4	5426
0.4-0.5	9630
0.5-0.6	10357
0.6-0.7	10380
0.7-0.8	2722
0.8-0.85	213
0.85-0.9	101
0.9-0.95	14
0.95-1	2

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 NPC481746 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	266
0.1-0.2	773
0.2-0.3	1614
0.3-0.4	2862
0.4-0.5	2214
0.5-0.6	1016
0.6-0.7	366
0.7-0.8	39
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