NPASS Compound

Structure

NPC64810 OpenBabel06302216202D 37 42 0 0 1 0 0 0 0 0999 V2000 4.2759 1.1630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4191 0.6754 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4130 -0.3104 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5563 -0.7980 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7056 -0.2998 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.7117 0.6859 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5685 1.1735 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8611 1.1841 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0043 0.6965 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5967 1.0485 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2021 0.7040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2064 0.0075 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9077 1.0038 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6053 -0.3445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6096 -1.0410 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2150 -1.3855 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8160 -1.0336 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8117 -0.3371 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2176 0.2289 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8787 0.4483 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5424 0.2371 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3409 0.6982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1210 0.2469 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1267 -0.6647 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9925 -0.6593 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5481 -0.6745 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5537 -1.5863 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.3338 -2.0376 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1323 -1.5766 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8926 -1.8056 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2289 -1.5945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6544 -2.3956 0.0000 O 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 0.8489 -0.7874 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5502 -1.7838 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4008 -2.2819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2637 -0.8085 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 37 1 1 0 0 0 4 5 1 0 0 0 0 4 35 1 6 0 0 0 5 6 1 0 0 0 0 5 34 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 1 0 0 0 9 8 1 6 0 0 0 9 10 1 0 0 0 0 9 33 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 18 1 0 0 0 0 12 13 1 6 0 0 0 12 14 1 0 0 0 0 14 15 2 0 0 0 0 14 33 1 0 0 0 0 15 16 1 0 0 0 0 17 16 1 1 0 0 0 17 18 1 0 0 0 0 17 31 1 0 0 0 0 18 19 1 6 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 29 1 0 0 0 0 24 25 1 1 0 0 0 24 26 1 0 0 0 0 26 21 1 6 0 0 0 26 27 1 0 0 0 0 27 28 1 6 0 0 0 27 30 1 0 0 0 0 28 29 1 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 35 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	520.27
Volume:	512.708
LogP:	2.668
LogD:	1.83
LogS:	-4.478
# Rotatable Bonds:	3
TPSA:	112.91
# H-Bond Aceptor:	9
# H-Bond Donor:	2
# Rings:	6
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.428
Synthetic Accessibility Score:	5.811
Fsp3:	0.821
Lipinski Rule-of-5:	Accepted
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:	-4.857
MDCK Permeability:	7.3143673944287e-05
Pgp-inhibitor:	0.962
Pgp-substrate:	0.901
Human Intestinal Absorption (HIA):	0.058
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.105

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.033
Plasma Protein Binding (PPB):	69.69873046875%
Volume Distribution (VD):	1.524
Pgp-substrate:	16.912078857421875%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.304
CYP2C19-inhibitor:	0.021
CYP2C19-substrate:	0.511
CYP2C9-inhibitor:	0.015
CYP2C9-substrate:	0.014
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.183
CYP3A4-inhibitor:	0.526
CYP3A4-substrate:	0.466

ADMET: Excretion

Clearance (CL):	1.717
Half-life (T1/2):	0.276

ADMET: Toxicity

hERG Blockers:	0.393
Human Hepatotoxicity (H-HT):	0.639
Drug-inuced Liver Injury (DILI):	0.411
AMES Toxicity:	0.257
Rat Oral Acute Toxicity:	0.798
Maximum Recommended Daily Dose:	0.87
Skin Sensitization:	0.063
Carcinogencity:	0.943
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.185

Download Data

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

Natural Product: NPC64810

Natural Product ID:	NPC64810
*Common Name:**	KBZJWPGSJWUHPT-PKTFCJAWSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KBZJWPGSJWUHPT-PKTFCJAWSA-N
Standard InCHI:	InChI=1S/C28H40O9/c1-14-22(29)24(32-4)23(30)26(35-14)36-17-9-10-27(2)16(11-17)6-7-18-19(27)8-5-15-12-33-28(3)21(15)20(13-34-28)37-25(18)31/h6,12,14,17-24,26,29-30H,5,7-11,13H2,1-4H3/t14-,17+,18-,19+,20-,21-,22-,23-,24+,26-,27+,28+/m1/s1
SMILES:	C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@H]1CC[C@@]2(C)C(=CC[C@@H]3[C@@H]2CCC2=CO[C@]4(C)[C@H]2[C@@H](CO4)OC3=O)C1)O)OC)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0002207] O-glycosyl 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
NPO25999	Ferula communis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15620264]
NPO26982	Callyspongia siphonella	Species	Callyspongiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17488128]
NPO26982	Callyspongia siphonella	Species	Callyspongiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[19534474]
NPO26953	Hebeloma senescens	Species	Cortinariaceae	Eukaryota	fruiting bodies	n.a.	n.a.	PMID[7561908]
NPO26455	Merwilla natalensis	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[Article]
NPO10658	Pedicularis rhinanthoides	Species	Orobanchaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26455	Merwilla natalensis	Species	Hyacinthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25900	Pteris podophylla	Species	Pteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25823	Haminoea navicula	Species	Haminoeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26324	Fevillea cordifolia	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25927	Dictyota dentata	Species	Dictyotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26885	Dictyosphaeria favulosa	Species	Siphonocladaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25874	Tuber borchii	Species	Tuberaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4538	Paysonia densipila	Species	Brassicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26809	Synoicum blochmanni	Species	Polyclinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26982	Callyspongia siphonella	Species	Callyspongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25999	Ferula communis	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26214	Baccharis artemisioides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26953	Hebeloma senescens	Species	Cortinariaceae	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 NPC64810 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	206
0.1-0.2	1234
0.2-0.3	4465
0.3-0.4	10691
0.4-0.5	11145
0.5-0.6	7401
0.6-0.7	6050
0.7-0.8	1443
0.8-0.85	52
0.85-0.9	7
0.9-0.95	2
0.95-1	1

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 NPC64810 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	173
0.1-0.2	1515
0.2-0.3	3980
0.3-0.4	2318
0.4-0.5	658
0.5-0.6	297
0.6-0.7	198
0.7-0.8	11
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