NPASS Compound

Structure

NPC130854 OpenBabel06302215552D 38 42 0 0 1 0 0 0 0 0999 V2000 2.7358 5.6930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2130 4.8663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1676 4.8663 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7358 4.0397 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7812 4.0397 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3039 4.8663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3494 4.8663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1279 4.0397 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1279 5.6930 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0 0.8267 2.3864 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3494 3.2130 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.9091 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8267 2.3864 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6533 1.9091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6533 0.9545 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4800 1.4318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4800 0.4773 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3066 0.9545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1787 0.5663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8174 1.2757 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3401 2.1023 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4064 1.9039 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4800 -0.4773 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6533 -0.9545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6533 -1.9091 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8267 -0.4773 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8267 0.4773 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 0.9545 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -0.9545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8267 0.4773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8267 -0.4773 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6533 0.9545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6533 1.9091 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4800 2.3864 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4345 2.3864 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9573 1.5597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4800 3.3409 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 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 1 0 0 0 5 10 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 10 33 1 0 0 0 0 10 11 1 6 0 0 0 10 12 1 0 0 0 0 12 13 1 6 0 0 0 12 28 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 27 1 0 0 0 0 15 16 1 1 0 0 0 15 17 1 0 0 0 0 17 18 1 1 0 0 0 17 23 1 0 0 0 0 18 22 2 0 0 0 0 18 19 1 0 0 0 0 19 20 2 0 0 0 0 20 21 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 26 24 1 6 0 0 0 26 27 1 0 0 0 0 26 38 1 0 0 0 0 27 28 1 0 0 0 0 27 38 1 6 0 0 0 28 29 1 6 0 0 0 28 30 1 0 0 0 0 30 31 2 0 0 0 0 30 32 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 6 0 0 0 34 35 1 0 0 0 0 34 36 1 0 0 0 0 34 37 1 0 0 0 0 M CHG 1 9 -1 M END $$$$

Physi-Chem Properties

Molecular Weight:	532.23
Volume:	522.145
LogP:	1.531
LogD:	0.781
LogS:	-3.78
# Rotatable Bonds:	7
TPSA:	152.87
# H-Bond Aceptor:	10
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.412
Synthetic Accessibility Score:	5.773
Fsp3:	0.714
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:	-5.496
MDCK Permeability:	1.8594739231048152e-05
Pgp-inhibitor:	0.193
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.042
20% Bioavailability (F20%):	0.877
30% Bioavailability (F30%):	0.93

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.157
Plasma Protein Binding (PPB):	70.89305877685547%
Volume Distribution (VD):	0.382
Pgp-substrate:	22.12322998046875%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.078
CYP2C19-inhibitor:	0.013
CYP2C19-substrate:	0.271
CYP2C9-inhibitor:	0.049
CYP2C9-substrate:	0.072
CYP2D6-inhibitor:	0.025
CYP2D6-substrate:	0.09
CYP3A4-inhibitor:	0.074
CYP3A4-substrate:	0.204

ADMET: Excretion

Clearance (CL):	3.722
Half-life (T1/2):	0.889

ADMET: Toxicity

hERG Blockers:	0.003
Human Hepatotoxicity (H-HT):	0.469
Drug-inuced Liver Injury (DILI):	0.898
AMES Toxicity:	0.145
Rat Oral Acute Toxicity:	0.949
Maximum Recommended Daily Dose:	0.591
Skin Sensitization:	0.176
Carcinogencity:	0.156
Eye Corrosion:	0.039
Eye Irritation:	0.271
Respiratory Toxicity:	0.921

Download Data

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

Natural Product: NPC130854

Natural Product ID:	NPC130854
*Common Name:**	ZIKZPLSIAVHITA-HNABCYPOSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ZIKZPLSIAVHITA-HNABCYPOSA-N
Standard InCHI:	InChI=1S/C28H36O10/c1-14(29)36-19(12-20(31)32)26(5)16-7-9-25(4)21(15-8-10-35-13-15)37-23(33)22-28(25,38-22)27(16,6)18(30)11-17(26)24(2,3)34/h8,10,13,16-17,19,21-22,34H,7,9,11-12H2,1-6H3,(H,31,32)/p-1/t16-,17+,19-,21+,22-,25+,26-,27+,28-/m1/s1
SMILES:	CC(=O)O[C@H](CC(=O)[O-])[C@]1(C)[C@H]2CC[C@@]3(C)[C@H](c4ccoc4)OC(=O)[C@@H]4[C@@]3([C@]2(C)C(=O)C[C@H]1C(C)(C)O)O4
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:0001125] Steroid lactones

*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
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12628396]
NPO2236	Pyrola rotundifolia	Species	Ericaceae	Eukaryota	n.a.	whole plant	n.a.	PMID[16079548]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	Hairy roots	n.a.	n.a.	PMID[19271765]
NPO5489	Cinnamomum tenuifolium	Species	Lauraceae	Eukaryota	stems	n.a.	n.a.	PMID[19754130]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	n.a.	leaf	n.a.	PMID[24024688]
NPO8528	Citrus junos	Species	Rutaceae	Eukaryota	n.a.	fruit	n.a.	PMID[25522543]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26285573]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6619887]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6631435]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7264679]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7264682]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7320741]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7798960]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2236	Pyrola rotundifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8528	Citrus junos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2236	Pyrola rotundifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8528	Citrus junos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11107	Stevia alpina	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7263	Phyllobates aurotaenia	Species	Dendrobatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5489	Cinnamomum tenuifolium	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29494	Stoeba extensa	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO7003	Streptomyces violaceochromogenes	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO8528	Citrus junos	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10402	Strophanthus eminii	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9919	Jaspis stellifera	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2236	Pyrola rotundifolia	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5881	Catharanthus roseus	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17324	Pluchea dioscoridis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9765	Petriella guttulata	Species	Microascaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4311	Asterolasia squamuligera	Species	Rutaceae	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 NPC130854 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	356
0.1-0.2	1445
0.2-0.3	3154
0.3-0.4	5758
0.4-0.5	10494
0.5-0.6	10271
0.6-0.7	9096
0.7-0.8	1709
0.8-0.85	245
0.85-0.9	100
0.9-0.95	49
0.95-1	20

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 NPC130854 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	301
0.1-0.2	1026
0.2-0.3	2152
0.3-0.4	2645
0.4-0.5	1887
0.5-0.6	848
0.6-0.7	260
0.7-0.8	29
0.8-0.85	2
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