NPASS Compound

Structure

NPC85091 OpenBabel06302215552D 53 57 0 0 1 0 0 0 0 0999 V2000 -1.2014 0.6553 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6353 -0.2457 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6325 -0.3204 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0719 -1.0719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0747 -0.9972 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1478 -1.9721 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7831 -2.3375 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6478 -2.8382 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.2256 -3.3251 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0324 -4.3063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9605 -4.4257 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3808 -3.5183 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2818 -3.9522 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2706 -4.1013 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.2595 -3.9522 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1604 -3.5183 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8935 -2.8382 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.3935 -1.9721 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.3244 -2.3375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4734 -3.3263 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4043 -3.6916 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.5533 -4.6805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7715 -5.3040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8406 -4.9386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6916 -3.9498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6160 -0.9972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5413 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.1759 0.9309 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 7.0420 1.4309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9080 0.9309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7740 1.4309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6400 0.9309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6400 -0.0691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7740 -0.5691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9080 -0.0691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5061 -0.5691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5525 1.7127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2326 2.4458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7262 2.2760 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.3018 3.0937 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7020 3.8939 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7557 3.5707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7706 2.5708 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.7706 2.5708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8151 2.2760 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.9888 1.7127 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3653 0.9309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.5007 1.4309 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6216 3.5596 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6132 -1.0719 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7238 -4.3446 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9871 -4.9078 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 2 4 1 0 0 0 0 5 4 1 6 0 0 0 5 6 1 0 0 0 0 5 48 1 0 0 0 0 6 7 2 0 0 0 0 6 8 1 0 0 0 0 8 12 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 12 11 1 6 0 0 0 12 13 1 0 0 0 0 13 14 2 3 0 0 0 13 53 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 3 0 0 0 16 52 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 18 26 1 0 0 0 0 19 20 1 0 0 0 0 20 25 2 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 2 0 0 0 0 24 25 1 0 0 0 0 26 27 2 3 0 0 0 26 51 1 0 0 0 0 27 28 1 0 0 0 0 28 29 1 6 0 0 0 28 37 1 0 0 0 0 29 30 1 0 0 0 0 30 35 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 36 1 0 0 0 0 34 35 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 39 43 1 0 0 0 0 39 40 1 0 0 0 0 40 41 1 0 0 0 0 41 42 1 0 0 0 0 43 42 1 6 0 0 0 43 44 1 0 0 0 0 44 45 2 3 0 0 0 44 50 1 0 0 0 0 45 46 1 0 0 0 0 46 47 1 0 0 0 0 47 48 2 3 0 0 0 47 49 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	731.36
Volume:	736.047
LogP:	0.404
LogD:	1.856
LogS:	-3.936
# Rotatable Bonds:	6
TPSA:	209.84
# H-Bond Aceptor:	15
# H-Bond Donor:	6
# Rings:	5
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.249
Synthetic Accessibility Score:	5.126
Fsp3:	0.5
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:	-6.618
MDCK Permeability:	5.271808277029777e-06
Pgp-inhibitor:	0.118
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.884
20% Bioavailability (F20%):	0.994
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.057
Plasma Protein Binding (PPB):	59.82383728027344%
Volume Distribution (VD):	0.444
Pgp-substrate:	36.09196472167969%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.013
CYP2C19-inhibitor:	0.094
CYP2C19-substrate:	0.044
CYP2C9-inhibitor:	0.197
CYP2C9-substrate:	0.422
CYP2D6-inhibitor:	0.012
CYP2D6-substrate:	0.143
CYP3A4-inhibitor:	0.676
CYP3A4-substrate:	0.027

ADMET: Excretion

Clearance (CL):	4.315
Half-life (T1/2):	0.864

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.996
Drug-inuced Liver Injury (DILI):	0.783
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.898
Maximum Recommended Daily Dose:	0.956
Skin Sensitization:	0.73
Carcinogencity:	0.107
Eye Corrosion:	0.003
Eye Irritation:	0.004
Respiratory Toxicity:	0.713

Download Data

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

Natural Product: NPC85091

Natural Product ID:	NPC85091
*Common Name:**	HHUIWONHQASLSE-QKUYTOGTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HHUIWONHQASLSE-QKUYTOGTSA-N
Standard InCHI:	InChI=1S/C38H49N7O8/c1-23(2)18-28-37(52)44-16-6-10-30(44)35(50)39-21-32(47)41-27(19-24-8-4-3-5-9-24)34(49)43-29(20-25-12-14-26(46)15-13-25)38(53)45-17-7-11-31(45)36(51)40-22-33(48)42-28/h3-5,8-9,12-15,23,27-31,46H,6-7,10-11,16-22H2,1-2H3,(H,39,50)(H,40,51)(H,41,47)(H,42,48)(H,43,49)/t27-,28-,29-,30-,31-/m0/s1
SMILES:	CC(C)C[C@H]1C(=O)N2CCC[C@H]2C(=NCC(=N[C@@H](Cc2ccccc2)C(=N[C@@H](Cc2ccc(cc2)O)C(=O)N2CCC[C@H]2C(=NCC(=N1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11422735
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000348] Peptides [CHEMONTID:0004831] Oligopeptides

*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
NPO2253	Illicium jiadifengpi	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11975494]
NPO2558	Ceratodictyon spongiosum	Species	Lomentariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19670881]
NPO7761	Laurencia majuscula	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8691206]
NPO3409	Goniothalamus leiocarpus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1536	Lindera triloba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO7761	Laurencia majuscula	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1093	Plumeria obtusa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7761	Laurencia majuscula	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3409	Goniothalamus leiocarpus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2253	Illicium jiadifengpi	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1536	Lindera triloba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2182	Athyrium filix-femina	Species	Athyriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7607	Ophiorrhiza pumila	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3409	Goniothalamus leiocarpus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO2253	Illicium jiadifengpi	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6838	Senecio grisebachii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1093	Plumeria obtusa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2182	Athyrium filix-femina	Species	Athyriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8060	Lethariella cashmeriana	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO274	Dendrobates viridis	Species	Dendrobatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7607	Ophiorrhiza pumila	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2956	Echinometra oblonga	Species	Echinometridae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11725	Cetonia aurata	Species	Scarabaeidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7450	Sida acuta	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3409	Goniothalamus leiocarpus	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5796	Haplopappus foliosus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5262	Sargassum natans	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1536	Lindera triloba	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2558	Ceratodictyon spongiosum	Species	Lomentariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7761	Laurencia majuscula	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4276	Cupressus lindleyi	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4805	Balanophora papuana	Species	Balanophoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1693	Gnomonia fragariae	Species	Sydowiellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1878	Kunzea baxteri	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3114	Stylocheilus striatus	Species	Aplysiidae	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 NPC85091 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	220
0.1-0.2	1034
0.2-0.3	5504
0.3-0.4	11583
0.4-0.5	14564
0.5-0.6	8273
0.6-0.7	1033
0.7-0.8	389
0.8-0.85	58
0.85-0.9	18
0.9-0.95	18
0.95-1	3

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 NPC85091 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	149
0.1-0.2	427
0.2-0.3	738
0.3-0.4	1586
0.4-0.5	3245
0.5-0.6	2374
0.6-0.7	581
0.7-0.8	48
0.8-0.85	1
0.85-0.9	0
0.9-0.95	1
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