NPASS Compound

Structure

NPC6635 OpenBabel06302216192D 37 40 0 0 1 0 0 0 0 0999 V2000 0.8459 1.5027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8462 0.4892 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0315 0.9959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6927 0.0005 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5395 0.4897 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3866 0.0010 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3869 -0.9770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5401 -1.4662 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5404 -2.4435 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3875 -2.9322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2343 -2.4430 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2346 -3.4565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0814 -2.9318 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.9270 -2.4426 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9267 -1.4652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2340 -1.4657 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.2337 -0.4522 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0816 -3.9087 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.0586 -3.9084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5473 -4.7543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5242 -4.7541 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 8.0125 -3.9079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9894 -3.9076 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4781 -4.7535 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.0129 -5.6000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0132 -6.5769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1670 -6.0887 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9899 -5.5997 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5934 -4.7549 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0821 -5.6008 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6165 -4.7552 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6930 -0.9775 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6933 -1.9775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8468 -1.4667 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 -0.9779 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8662 0.4996 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 36 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 6 0 0 0 4 32 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 16 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 32 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 16 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 13 14 1 0 0 0 0 13 18 1 1 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 6 0 0 0 18 19 1 6 0 0 0 18 29 1 0 0 0 0 19 20 1 0 0 0 0 21 20 1 1 0 0 0 21 22 1 0 0 0 0 21 25 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 25 26 1 0 0 0 0 25 27 1 0 0 0 0 25 28 1 0 0 0 0 29 30 2 0 0 0 0 29 31 1 0 0 0 0 32 33 1 6 0 0 0 32 34 1 0 0 0 0 34 35 1 0 0 0 0 35 36 1 0 0 0 0 36 37 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	682.34
Volume:	684.146
LogP:	4.426
LogD:	3.662
LogS:	-4.048
# Rotatable Bonds:	8
TPSA:	179.28
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	7
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.139
Synthetic Accessibility Score:	5.308
Fsp3:	0.658
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.915
MDCK Permeability:	1.599061033630278e-05
Pgp-inhibitor:	0.053
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.949
20% Bioavailability (F20%):	0.995
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.181
Plasma Protein Binding (PPB):	98.96929168701172%
Volume Distribution (VD):	0.818
Pgp-substrate:	2.6046595573425293%

ADMET: Metabolism

CYP1A2-inhibitor:	0.034
CYP1A2-substrate:	0.13
CYP2C19-inhibitor:	0.076
CYP2C19-substrate:	0.1
CYP2C9-inhibitor:	0.3
CYP2C9-substrate:	0.186
CYP2D6-inhibitor:	0.03
CYP2D6-substrate:	0.272
CYP3A4-inhibitor:	0.637
CYP3A4-substrate:	0.147

ADMET: Excretion

Clearance (CL):	5.361
Half-life (T1/2):	0.634

ADMET: Toxicity

hERG Blockers:	0.764
Human Hepatotoxicity (H-HT):	0.226
Drug-inuced Liver Injury (DILI):	0.019
AMES Toxicity:	0.047
Rat Oral Acute Toxicity:	0.32
Maximum Recommended Daily Dose:	0.96
Skin Sensitization:	0.959
Carcinogencity:	0.4
Eye Corrosion:	0.003
Eye Irritation:	0.012
Respiratory Toxicity:	0.954

Download Data

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

Natural Product: NPC6635

Natural Product ID:	NPC6635
*Common Name:**	NXQZDWWJEWCQPT-TVXBYUSTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NXQZDWWJEWCQPT-TVXBYUSTSA-N
Standard InCHI:	InChI=1S/C32H54O5/c1-28(2)25-11-10-24-23(30(25,5)16-14-26(28)34)13-18-31(6)22(12-17-32(24,31)7)21(27(35)36)9-8-20(15-19-33)29(3,4)37/h20-22,25-26,33-34,37H,8-19H2,1-7H3,(H,35,36)/t20-,21-,22-,25-,26+,30+,31-,32+/m0/s1
SMILES:	CC1(C)[C@@H]2CCC3=C(CC[C@@]4(C)[C@@H](CC[C@]34C)[C@H](CC[C@@H](CCO)C(C)(C)O)C(=O)O)[C@@]2(C)CC[C@H]1O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002031] Stigmastanes 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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19919095]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	flower buds and leaves	Khon Kaen province, Thailand	2010	PMID[23270663]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[23642481]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[26462418]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Rhizome	n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21728	Iva asperifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3478	Nelumbo nucifera	Species	Nelumbonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1862	Helichrysum platypterum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22120	Tanacetum aucherianum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21728	Iva asperifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22379	Thymus caespititius	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28031	Calocedrus decurrens	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16195	Sclerotinia sclerotiorum	Species	Sclerotiniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22313	Aspilia eenii	Species	Asteraceae	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 NPC6635 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	177
0.1-0.2	1366
0.2-0.3	5821
0.3-0.4	15251
0.4-0.5	6710
0.5-0.6	5907
0.6-0.7	5497
0.7-0.8	1722
0.8-0.85	170
0.85-0.9	58
0.9-0.95	18
0.95-1	0

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 NPC6635 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	154
0.1-0.2	1893
0.2-0.3	4036
0.3-0.4	2073
0.4-0.5	542
0.5-0.6	150
0.6-0.7	184
0.7-0.8	118
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