NPASS Compound

Structure

NPC128515 OpenBabel06302215542D 36 40 0 0 1 0 0 0 0 0999 V2000 4.0523 -1.3619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5461 -0.4862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5346 -0.4868 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0398 0.3895 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5352 -1.4624 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6906 -1.9507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8454 -1.4634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8449 -0.4878 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0253 -0.9908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6895 0.0005 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6892 0.9765 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8443 1.4643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0003 0.9760 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0006 1.9811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8457 1.4638 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8460 2.4393 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6915 2.9271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5367 2.4388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5364 1.4633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2258 1.4629 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9363 0.7520 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2261 2.4383 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3821 2.9266 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3827 3.9317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6909 0.9756 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5612 0.4728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6906 -0.0005 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8452 -0.4883 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5358 -0.4887 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9325 -1.3805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9032 -1.4828 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3586 -2.1700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7554 -3.0618 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7261 -3.1640 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1815 -3.8513 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 3 10 1 0 0 0 0 3 4 1 6 0 0 0 3 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 29 1 0 0 0 0 8 9 1 1 0 0 0 8 10 1 0 0 0 0 10 11 1 1 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 29 1 0 0 0 0 13 14 1 1 0 0 0 13 15 1 0 0 0 0 15 16 1 1 0 0 0 15 25 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 18 23 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 19 25 1 0 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 1 0 0 0 25 26 1 1 0 0 0 25 27 1 0 0 0 0 27 28 1 0 0 0 0 27 30 1 6 0 0 0 29 28 1 1 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 33 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 1 0 0 0 34 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	500.35
Volume:	537.991
LogP:	6.0
LogD:	4.442
LogS:	-5.218
# Rotatable Bonds:	5
TPSA:	79.9
# H-Bond Aceptor:	5
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.443
Synthetic Accessibility Score:	5.137
Fsp3:	0.839
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:	-4.907
MDCK Permeability:	2.7854341169586405e-05
Pgp-inhibitor:	0.993
Pgp-substrate:	0.025
Human Intestinal Absorption (HIA):	0.005
20% Bioavailability (F20%):	0.005
30% Bioavailability (F30%):	0.847

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.393
Plasma Protein Binding (PPB):	91.7160873413086%
Volume Distribution (VD):	1.076
Pgp-substrate:	3.306049108505249%

ADMET: Metabolism

CYP1A2-inhibitor:	0.033
CYP1A2-substrate:	0.253
CYP2C19-inhibitor:	0.025
CYP2C19-substrate:	0.881
CYP2C9-inhibitor:	0.155
CYP2C9-substrate:	0.157
CYP2D6-inhibitor:	0.011
CYP2D6-substrate:	0.268
CYP3A4-inhibitor:	0.625
CYP3A4-substrate:	0.548

ADMET: Excretion

Clearance (CL):	15.943
Half-life (T1/2):	0.1

ADMET: Toxicity

hERG Blockers:	0.414
Human Hepatotoxicity (H-HT):	0.392
Drug-inuced Liver Injury (DILI):	0.17
AMES Toxicity:	0.008
Rat Oral Acute Toxicity:	0.472
Maximum Recommended Daily Dose:	0.885
Skin Sensitization:	0.914
Carcinogencity:	0.407
Eye Corrosion:	0.008
Eye Irritation:	0.016
Respiratory Toxicity:	0.974

Download Data

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

Natural Product: NPC128515

Natural Product ID:	NPC128515
*Common Name:**	YKTARPGVJCHEQJ-YMDJUAKCSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YKTARPGVJCHEQJ-YMDJUAKCSA-N
Standard InCHI:	InChI=1S/C31H48O5/c1-8-28(4)13-9-14-29(5)21(28)12-15-30(6)22-11-10-20-19(3)35-27(34)26(20)31(22,7)24(17-23(29)30)36-25(33)16-18(2)32/h18-19,21-24,32H,8-17H2,1-7H3/t18-,19-,21-,22-,23+,24-,28-,29-,30-,31+/m0/s1
SMILES:	CC[C@@]1(C)CCC[C@@]2(C)[C@H]1CC[C@@]1(C)[C@@H]3CCC4=C(C(=O)O[C@H]4C)[C@@]3(C)[C@H](C[C@H]21)OC(=O)C[C@H](C)O
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:0000259] Prenol lipids [CHEMONTID:0001552] Sesterterpenoids [CHEMONTID:0002883] Scalarane sesterterpenoids

*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
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[11374978]
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15679317]
NPO4645	Grewia bilamellata	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[16562832]
NPO16258	Holothuria fuscocinerea	Species	Holothuriidae	Eukaryota	n.a.	collected at a depth of 2-30 m by a fishery bottom trawler from offshore waters of Leizhou Bay (Zhanjiang, Guangdong Province) in the South China Sea	2004-NOV	PMID[17067169]
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota	n.a.	root	n.a.	PMID[17997069]
NPO4250	Gloriosa superba	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32372642]
NPO4250	Gloriosa superba	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4250	Gloriosa superba	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO4250	Gloriosa superba	Species	Colchicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4645	Grewia bilamellata	Species	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO11438	Angelica gigas	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16258	Holothuria fuscocinerea	Species	Holothuriidae	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 NPC128515 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	240
0.1-0.2	1448
0.2-0.3	4336
0.3-0.4	8672
0.4-0.5	12623
0.5-0.6	6706
0.6-0.7	5620
0.7-0.8	2823
0.8-0.85	188
0.85-0.9	21
0.9-0.95	8
0.95-1	12

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 NPC128515 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	213
0.1-0.2	1749
0.2-0.3	3594
0.3-0.4	2298
0.4-0.5	820
0.5-0.6	231
0.6-0.7	189
0.7-0.8	55
0.8-0.85	1
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