NPASS Compound

Structure

NPC7456 OpenBabel06302216152D 43 49 0 0 1 0 0 0 0 0999 V2000 -9.3618 1.8333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.3618 2.8166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5663 3.3946 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6311 3.0908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9004 3.7487 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9652 3.4449 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.7607 2.4831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1137 3.9366 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1131 4.9199 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2612 5.4117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4093 3.9363 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5568 3.4441 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5568 2.4598 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4087 1.9679 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2612 2.4601 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.2612 3.4444 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1300 2.9427 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1136 1.9679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1136 0.9836 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9660 0.4914 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2611 0.4914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7043 1.9676 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5716 1.4669 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7046 0.9838 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8524 0.4921 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 0.9843 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0002 1.9681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8519 2.4598 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8519 3.4441 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7044 3.9363 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8519 4.4284 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0154 2.9605 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 -2.5566 0.4919 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5404 0.4918 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0323 -0.3602 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0323 1.3438 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9790 5.4201 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1048 4.7106 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.8702 4.3298 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.8535 4.3298 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.1573 3.3946 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.0925 3.0907 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 42 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 40 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 5 39 1 1 0 0 0 6 7 1 6 0 0 0 8 6 1 1 0 0 0 8 9 1 0 0 0 0 8 16 1 0 0 0 0 9 10 1 0 0 0 0 9 38 1 6 0 0 0 11 10 1 1 0 0 0 11 12 1 0 0 0 0 11 16 1 0 0 0 0 12 13 1 0 0 0 0 12 30 1 0 0 0 0 13 14 1 1 0 0 0 13 22 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 18 1 6 0 0 0 16 17 1 1 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 19 21 1 0 0 0 0 22 28 1 0 0 0 0 22 23 1 1 0 0 0 22 24 1 0 0 0 0 24 25 1 0 0 0 0 24 34 1 6 0 0 0 25 26 1 0 0 0 0 25 33 1 6 0 0 0 26 27 1 6 0 0 0 26 33 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 0 0 0 0 28 32 1 6 0 0 0 29 30 1 0 0 0 0 29 31 1 6 0 0 0 30 31 1 6 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 35 37 1 0 0 0 0 40 41 1 0 0 0 0 41 42 1 0 0 0 0 42 43 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	604.29
Volume:	588.279
LogP:	3.034
LogD:	2.666
LogS:	-4.236
# Rotatable Bonds:	8
TPSA:	171.72
# H-Bond Aceptor:	11
# H-Bond Donor:	4
# Rings:	7
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.277
Synthetic Accessibility Score:	6.033
Fsp3:	0.812
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:	-6.137
MDCK Permeability:	9.089828381547704e-05
Pgp-inhibitor:	0.163
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.833
20% Bioavailability (F20%):	0.01
30% Bioavailability (F30%):	0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.145
Plasma Protein Binding (PPB):	63.08800506591797%
Volume Distribution (VD):	0.535
Pgp-substrate:	24.14596176147461%

ADMET: Metabolism

CYP1A2-inhibitor:	0.015
CYP1A2-substrate:	0.042
CYP2C19-inhibitor:	0.009
CYP2C19-substrate:	0.074
CYP2C9-inhibitor:	0.012
CYP2C9-substrate:	0.044
CYP2D6-inhibitor:	0.035
CYP2D6-substrate:	0.097
CYP3A4-inhibitor:	0.16
CYP3A4-substrate:	0.23

ADMET: Excretion

Clearance (CL):	3.009
Half-life (T1/2):	0.878

ADMET: Toxicity

hERG Blockers:	0.4
Human Hepatotoxicity (H-HT):	0.357
Drug-inuced Liver Injury (DILI):	0.277
AMES Toxicity:	0.03
Rat Oral Acute Toxicity:	0.851
Maximum Recommended Daily Dose:	0.035
Skin Sensitization:	0.316
Carcinogencity:	0.229
Eye Corrosion:	0.011
Eye Irritation:	0.011
Respiratory Toxicity:	0.981

Download Data

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

Natural Product: NPC7456

Natural Product ID:	NPC7456
*Common Name:**	XLECXEWCXHZSAY-MMAXEIPCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	XLECXEWCXHZSAY-MMAXEIPCSA-N
Standard InCHI:	InChI=1S/C32H44O11/c1-12-16(11-39-29(12)37)7-19(35)13(2)24-20(36)8-17-23-18(9-22(30(17,24)5)40-14(3)33)31(6)27(41-15(4)34)25-21(42-25)10-32(31,38)28-26(23)43-28/h13,17-28,35-36,38H,7-11H2,1-6H3/t13-,17+,18+,19-,20-,21+,22+,23+,24+,25+,26+,27+,28+,30-,31+,32+/m1/s1
SMILES:	CC1=C(C[C@H]([C@@H](C)[C@H]2[C@@H](C[C@H]3[C@H]4[C@H](C[C@@H]([C@]23C)OC(=O)C)[C@@]2(C)[C@H]([C@@H]3[C@H](C[C@@]2([C@@H]2[C@H]4O2)O)O3)OC(=O)C)O)O)COC1=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101198624
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001445] Bile acids, alcohols 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
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[10230514]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	rhizomes	SiMao City, Yunnan Province, China	1996-OCT	PMID[11908966]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	Rhizomes	n.a.	n.a.	PMID[12350150]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12956064]
NPO12186	Oplopanax chironium	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15104479]
NPO11157	Corydalis saxicola	Species	Papaveraceae	Eukaryota	n.a.	root	n.a.	PMID[17611928]
NPO11157	Corydalis saxicola	Species	Papaveraceae	Eukaryota	n.a.	leaf	n.a.	PMID[18649321]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20715765]
NPO7143	Acacia jacquemontii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21894904]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25608854]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[33253561]
NPO13831	Cephalotaxus oliveri	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13426	Lemmaphyllum microphyllum	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10695	Pelargonium zonale	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10695	Pelargonium zonale	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13426	Lemmaphyllum microphyllum	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO13831	Cephalotaxus oliveri	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12093	Papaver orientale	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10695	Pelargonium zonale	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3227	Androsace umbellata	Species	Primulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8399	Psiadia trinervia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1576	Anthriscus sylvestris	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11157	Corydalis saxicola	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7143	Acacia jacquemontii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14634	Artemisia balchanorum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1133	Zieria laevigata	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11753	Sideroxylon foetidissimum	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6266	Anzia hypoleucoides	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9487	Penicillium flexuosum	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5551	Podocarpus sylvestris	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13831	Cephalotaxus oliveri	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11396	Metzgeria furcata	Species	Metzgeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14018	Pleurotus salmoneostramineus	Species	Pleurotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11909	Othonna arborescens	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14308	Coleonema pulchrum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9126	Stevia maimarensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12268	Aloe littoralis	Species	Asphodelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12093	Papaver orientale	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13332	Tacca chantrieri	Species	Taccaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12186	Oplopanax chironium	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13527	Solanum ecuadorense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13723	Salvia eriophora	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13426	Lemmaphyllum microphyllum	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10695	Pelargonium zonale	Species	Geraniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11585	Geijera salicifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10094	Daphne gnidioides	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

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 NPC7456 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	291
0.1-0.2	1978
0.2-0.3	5618
0.3-0.4	11731
0.4-0.5	10169
0.5-0.6	6452
0.6-0.7	5060
0.7-0.8	1282
0.8-0.85	111
0.85-0.9	5
0.9-0.95	0
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 NPC7456 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	271
0.1-0.2	2202
0.2-0.3	4061
0.3-0.4	1774
0.4-0.5	453
0.5-0.6	252
0.6-0.7	114
0.7-0.8	18
0.8-0.85	5
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