NPASS Compound

Structure

NPC113170 OpenBabel06302215382D 32 36 0 0 1 0 0 0 0 0999 V2000 2.7974 3.3358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7531 2.8029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6924 3.3642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7694 1.7089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7251 1.1760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7415 0.0820 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6972 -0.4509 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4050 -1.1866 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6476 -1.4169 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.5852 -2.2061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0560 -3.1938 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6760 -2.2923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8706 -2.5467 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2184 -2.0981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2807 -1.3089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9953 -0.9683 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.0895 -0.9728 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9393 -0.1787 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2354 0.2860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1598 1.1260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1354 1.5105 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1878 0.9634 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2402 1.5105 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7076 0.9633 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.7075 -0.1311 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2400 -0.6782 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1878 -0.1310 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.1230 -0.4375 0.0000 C 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 -0.4920 -0.8523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4920 0.8523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2400 -1.6623 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 4 20 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 18 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 9 8 1 1 0 0 0 9 10 1 0 0 0 0 9 16 1 0 0 0 0 10 11 1 0 0 0 0 10 12 1 0 0 0 0 10 13 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 16 17 1 1 0 0 0 16 18 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 21 1 0 0 0 0 22 21 1 6 0 0 0 22 23 1 0 0 0 0 22 27 1 0 0 0 0 24 23 1 1 0 0 0 24 25 1 0 0 0 0 24 29 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 26 32 1 6 0 0 0 27 28 1 6 0 0 0 27 29 1 0 0 0 0 29 30 1 0 0 0 0 29 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	438.35
Volume:	494.325
LogP:	7.946
LogD:	5.531
LogS:	-7.323
# Rotatable Bonds:	3
TPSA:	29.46
# H-Bond Aceptor:	2
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	2

MedChem Properties

QED Drug-Likeness Score:	0.532
Synthetic Accessibility Score:	5.244
Fsp3:	0.8
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.062
MDCK Permeability:	1.079484627553029e-05
Pgp-inhibitor:	0.996
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.013
20% Bioavailability (F20%):	0.991
30% Bioavailability (F30%):	0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.091
Plasma Protein Binding (PPB):	97.67508697509766%
Volume Distribution (VD):	2.093
Pgp-substrate:	2.4821176528930664%

ADMET: Metabolism

CYP1A2-inhibitor:	0.067
CYP1A2-substrate:	0.476
CYP2C19-inhibitor:	0.142
CYP2C19-substrate:	0.948
CYP2C9-inhibitor:	0.139
CYP2C9-substrate:	0.842
CYP2D6-inhibitor:	0.303
CYP2D6-substrate:	0.877
CYP3A4-inhibitor:	0.579
CYP3A4-substrate:	0.655

ADMET: Excretion

Clearance (CL):	8.059
Half-life (T1/2):	0.015

ADMET: Toxicity

hERG Blockers:	0.855
Human Hepatotoxicity (H-HT):	0.096
Drug-inuced Liver Injury (DILI):	0.581
AMES Toxicity:	0.012
Rat Oral Acute Toxicity:	0.724
Maximum Recommended Daily Dose:	0.992
Skin Sensitization:	0.384
Carcinogencity:	0.132
Eye Corrosion:	0.007
Eye Irritation:	0.638
Respiratory Toxicity:	0.791

Download Data

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

Natural Product: NPC113170

Natural Product ID:	NPC113170
*Common Name:**	UIKNKYMMENGHMR-XBTLXHJMSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UIKNKYMMENGHMR-XBTLXHJMSA-N
Standard InCHI:	InChI=1S/C30H46O2/c1-18(2)21-14-19-10-11-24-27(3,4)12-9-13-29(24,7)22(19)17-23(21)32-26-16-20-15-25(31)30(26,8)28(20,5)6/h14,17-18,20,24-26,31H,9-13,15-16H2,1-8H3/t20-,24-,25+,26-,29+,30+/m0/s1
SMILES:	CC(C)c1cc2CC[C@H]3C(C)(C)CCC[C@]3(C)c2cc1O[C@H]1C[C@@H]2C[C@H]([C@@]1(C)C2(C)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11553935
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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
NPO17318	Streptomyces cyaneus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21462031]
NPO15612	Glaucium oxylobum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15612	Glaucium oxylobum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15612	Glaucium oxylobum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3705	Anacardium humile	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13361	Clerodendrum tomentosum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17158	Trichocereus bridgesii	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17318	Streptomyces cyaneus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO5124	Aconitum ibukiense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12311	Graphis handelii	Species	Graphidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14653	Haliotis diversicolor	Species	Haliotidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14339	Fevillea trilobata	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25141	Mycetinis alliaceus	Species	Omphalotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15612	Glaucium oxylobum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17251	Aniba firmula	Species	Lauraceae	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 NPC113170 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	452
0.1-0.2	1407
0.2-0.3	3352
0.3-0.4	7533
0.4-0.5	11157
0.5-0.6	8167
0.6-0.7	9081
0.7-0.8	1527
0.8-0.85	19
0.85-0.9	2
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 NPC113170 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	352
0.1-0.2	850
0.2-0.3	1733
0.3-0.4	2709
0.4-0.5	1958
0.5-0.6	1085
0.6-0.7	398
0.7-0.8	58
0.8-0.85	4
0.85-0.9	2
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