NPASS Compound

Structure

CID12016 OpenBabel06191715342D 44 47 0 0 1 0 0 0 0 0999 V2000 0.8133 2.3478 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2459 -1.0318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9180 -2.5551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4654 -0.9092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8075 -2.1542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8390 1.6842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1984 0.8166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5717 0.7451 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5065 0.9391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5065 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6932 1.4087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6932 -0.4696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8799 0.9391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0666 -0.4696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2533 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6266 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8133 -0.4696 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9734 1.1563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8133 1.4087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5059 -0.1294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6631 -1.9834 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8937 -1.6543 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8764 -2.2768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8799 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6032 1.6032 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6266 0.9391 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9301 0.3852 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2533 0.9391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.9391 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2673 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6641 1.6032 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6032 -0.6641 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6641 -0.6641 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2673 0.9391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.5308 -2.3428 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2531 -2.5219 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5170 -3.1444 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0666 1.4087 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3047 2.4709 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5405 -1.0523 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.9626 -1.5317 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3047 -1.5317 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4399 1.4087 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 19 2 0 0 0 0 2 20 1 0 0 0 0 3 21 1 0 0 0 0 4 22 1 0 0 0 0 5 23 1 0 0 0 0 6 34 1 0 0 0 0 7 34 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 10 12 1 0 0 0 0 11 13 2 0 0 0 0 12 24 2 0 0 0 0 13 24 1 0 0 0 0 14 15 2 0 0 0 0 14 24 1 0 0 0 0 15 28 1 0 0 0 0 16 17 1 0 0 0 0 16 26 1 0 0 0 0 17 35 1 0 0 0 0 18 27 1 0 0 0 0 19 26 1 0 0 0 0 19 29 1 0 0 0 0 20 27 1 0 0 0 0 20 30 2 0 0 0 0 21 36 2 0 0 0 0 21 41 1 0 0 0 0 22 37 2 0 0 0 0 22 42 1 0 0 0 0 23 38 2 0 0 0 0 23 43 1 0 0 0 0 25 18 1 1 0 0 0 25 31 1 0 0 0 0 25 34 1 0 0 0 0 26 44 1 1 0 0 0 27 41 1 6 0 0 0 28 39 2 0 0 0 0 28 44 1 0 0 0 0 29 31 1 0 0 0 0 29 35 1 6 0 0 0 30 32 1 0 0 0 0 30 34 1 0 0 0 0 31 40 1 1 0 0 0 32 33 1 0 0 0 0 32 42 1 6 0 0 0 33 35 1 1 0 0 0 33 43 1 0 0 0 0 35 8 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	608.3
Volume:	632.438
LogP:	4.471
LogD:	3.231
LogS:	-4.971
# Rotatable Bonds:	10
TPSA:	125.43
# H-Bond Aceptor:	9
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.203
Synthetic Accessibility Score:	5.605
Fsp3:	0.543
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:	-4.952
MDCK Permeability:	8.493602217640728e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.997
Human Intestinal Absorption (HIA):	0.047
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.964

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.084
Plasma Protein Binding (PPB):	83.85364532470703%
Volume Distribution (VD):	2.617
Pgp-substrate:	10.62100601196289%

ADMET: Metabolism

CYP1A2-inhibitor:	0.117
CYP1A2-substrate:	0.032
CYP2C19-inhibitor:	0.134
CYP2C19-substrate:	0.067
CYP2C9-inhibitor:	0.736
CYP2C9-substrate:	0.106
CYP2D6-inhibitor:	0.662
CYP2D6-substrate:	0.085
CYP3A4-inhibitor:	0.736
CYP3A4-substrate:	0.428

ADMET: Excretion

Clearance (CL):	3.265
Half-life (T1/2):	0.012

ADMET: Toxicity

hERG Blockers:	0.06
Human Hepatotoxicity (H-HT):	0.956
Drug-inuced Liver Injury (DILI):	0.961
AMES Toxicity:	0.043
Rat Oral Acute Toxicity:	0.363
Maximum Recommended Daily Dose:	0.951
Skin Sensitization:	0.1
Carcinogencity:	0.068
Eye Corrosion:	0.015
Eye Irritation:	0.046
Respiratory Toxicity:	0.959

Download Data

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

Natural Product: NPC12016

Natural Product ID:	NPC12016
*Common Name:**	NQINDQGQJLIYFL-PBRGCZQGSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	NQINDQGQJLIYFL-PBRGCZQGSA-N
Standard InCHI:	InChI=1S/C35H44O9/c1-19-26(44-28(39)15-14-24-12-10-9-11-13-24)16-17-35(8)29(19)31(40)25-18-27(41-21(3)36)20(2)30(34(25,6)7)32(42-22(4)37)33(35)43-23(5)38/h9-15,25-27,29,31-33,40H,1,16-18H2,2-8H3/b15-14+/t25-,26-,27-,29-,31+,32+,33-,35+/m0/s1
SMILES:	CC(=O)O[C@H]1[C@H](OC(=O)C)C2=C(C)[C@@H](OC(=O)C)C[C@H](C2(C)C)[C@H]([C@H]2[C@@]1(C)CC[C@@H](C2=C)OC(=O)/C=C/c1ccccc1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL39025
PubChem CID:	9916874
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0000676] Taxanes and derivatives

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO33211	japanese yew	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[9873389]
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	xylem	n.a.	PMID[21138310]
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	wood	Yunnang Province, China	2000-OCT	PMID[21138310]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15974623]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	Japan	n.a.	PMID[15974623]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15844936]
NPO24820	Taxus cuspidata	Species	Taxaceae	Eukaryota	n.a.	Japan	n.a.	PMID[14987066]
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	wood	n.a.	n.a.	PMID[12444707]
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12217376]
NPO31343	Taxus chinensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12217376]

Showing 1 to 10 of 20 entries

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

Activity Type	# Activity
ED50	3
IC50	2
Others	4

Activity Type	# Activity
Cell Line	3
Individual Protein	2
NON-MOLECULAR	1
Others	3

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT668	Individual Protein	P-glycoprotein 1	Homo sapiens	Inhibition	=	670.0	%	PMID[479057]
NPT668	Individual Protein	P-glycoprotein 1	Homo sapiens	Inhibition	=	323.0	%	PMID[479057]
NPT137	Cell Line	L1210	Mus musculus	IC50	=	5.8	ug.mL-1	PMID[479056]
NPT2	Others	Unspecified	""	VCR accumulation	=	419.0	n.a.	PMID[479056]
NPT2	Others	Unspecified	""	VCR accumulation	=	873.0	n.a.	PMID[479056]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	9.2	ug.mL-1	PMID[479056]
NPT1178	Cell Line	KB 3-1	Homo sapiens	ED50	=	11.0	ug ml-1	PMID[479055]
NPT1178	Cell Line	KB 3-1	Homo sapiens	ED50	=	9.4	ug ml-1	PMID[479055]
NPT27	Others	Unspecified	""	ED50	=	12.5	ug ml-1	PMID[479055]

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☑ 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 NPC12016 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	222
0.1-0.2	961
0.2-0.3	2013
0.3-0.4	5262
0.4-0.5	9349
0.5-0.6	18780
0.6-0.7	5444
0.7-0.8	607
0.8-0.85	35
0.85-0.9	10
0.9-0.95	9
0.95-1	5

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Similarity Score	Similarity Level	Natural Product ID
0.9914	High Similarity	NPC472373
0.9829	High Similarity	NPC471758
0.9746	High Similarity	NPC45821
0.9565	High Similarity	NPC89324
0.9487	High Similarity	NPC473439

Showing 1 to 5 of 200 entries

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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 NPC12016 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	201
0.1-0.2	702
0.2-0.3	1418
0.3-0.4	2997
0.4-0.5	2195
0.5-0.6	1456
0.6-0.7	173
0.7-0.8	8
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7483	Intermediate Similarity	NPD7274	Clinical (unspecified phase)
0.748	Intermediate Similarity	NPD4198	Discontinued
0.7442	Intermediate Similarity	NPD7741	Discontinued
0.7328	Intermediate Similarity	NPD5126	Approved
0.7328	Intermediate Similarity	NPD5125	Phase 3

Showing 1 to 5 of 200 entries

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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