NPASS Compound

Structure

NPC221895 OpenBabel06302215382D 48 52 0 0 1 0 0 0 0 0999 V2000 3.6744 3.2471 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7213 3.0145 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3492 2.1066 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9019 1.2960 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.6127 0.3584 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.6994 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.2737 0.8840 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6994 -0.9811 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.8497 -1.4717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9811 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -0.9811 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9811 -0.9811 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8497 0.4906 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.7035 1.4607 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.3708 2.1800 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.1382 3.1331 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9728 3.6489 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 2.0461 4.6273 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9402 1.2983 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0082 0.3196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8219 0.8678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0385 1.2304 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2341 1.7499 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4524 2.7065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2668 3.3738 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3900 2.9957 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2539 0.9477 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1336 2.3352 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0813 2.0813 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8797 3.2829 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5491 -1.4717 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5491 -2.4528 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3987 -2.9434 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6994 -2.9434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3319 -0.3089 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2694 -0.0197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4878 0.9368 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9887 -0.6870 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8720 1.4422 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2305 2.3555 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6188 3.1226 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2007 2.5018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8124 1.7347 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7826 1.8809 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1410 2.7942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5293 3.5613 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5591 3.4151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 18 1 0 0 0 0 2 3 2 0 0 0 0 3 16 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 4 40 1 0 0 0 0 5 6 1 0 0 0 0 5 36 1 0 0 0 0 6 14 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 8 9 1 0 0 0 0 8 32 1 0 0 0 0 9 10 1 0 0 0 0 10 13 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 14 1 0 0 0 0 11 28 1 0 0 0 0 12 13 1 0 0 0 0 14 15 1 0 0 0 0 15 16 1 0 0 0 0 15 24 1 0 0 0 0 16 17 1 0 0 0 0 16 20 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 0 0 0 0 20 21 1 0 0 0 0 20 22 1 0 0 0 0 20 23 1 0 0 0 0 24 25 1 0 0 0 0 25 26 2 0 0 0 0 25 27 1 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 29 31 1 0 0 0 0 32 33 1 0 0 0 0 33 34 2 0 0 0 0 33 35 1 0 0 0 0 36 37 1 0 0 0 0 37 38 2 0 0 0 0 37 39 1 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 41 43 1 0 0 0 0 43 48 2 0 0 0 0 43 44 1 0 0 0 0 44 45 2 0 0 0 0 45 46 1 0 0 0 0 46 47 2 0 0 0 0 47 48 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	672.28
Volume:	661.678
LogP:	2.086
LogD:	1.909
LogS:	-4.296
# Rotatable Bonds:	12
TPSA:	181.19
# H-Bond Aceptor:	13
# H-Bond Donor:	2
# Rings:	5
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.245
Synthetic Accessibility Score:	5.243
Fsp3:	0.629
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:	-5.285
MDCK Permeability:	0.00014496207586489618
Pgp-inhibitor:	1.0
Pgp-substrate:	0.994
Human Intestinal Absorption (HIA):	0.959
20% Bioavailability (F20%):	0.964
30% Bioavailability (F30%):	0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.383
Plasma Protein Binding (PPB):	43.14280700683594%
Volume Distribution (VD):	1.105
Pgp-substrate:	29.855913162231445%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.027
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.104
CYP2C9-inhibitor:	0.052
CYP2C9-substrate:	0.053
CYP2D6-inhibitor:	0.035
CYP2D6-substrate:	0.057
CYP3A4-inhibitor:	0.196
CYP3A4-substrate:	0.412

ADMET: Excretion

Clearance (CL):	2.227
Half-life (T1/2):	0.077

ADMET: Toxicity

hERG Blockers:	0.005
Human Hepatotoxicity (H-HT):	0.917
Drug-inuced Liver Injury (DILI):	0.934
AMES Toxicity:	0.02
Rat Oral Acute Toxicity:	0.916
Maximum Recommended Daily Dose:	0.308
Skin Sensitization:	0.011
Carcinogencity:	0.034
Eye Corrosion:	0.003
Eye Irritation:	0.007
Respiratory Toxicity:	0.016

Download Data

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

Natural Product: NPC221895

Natural Product ID:	NPC221895
*Common Name:**	IKDVXNASCSGIHM-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	IKDVXNASCSGIHM-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C35H44O13/c1-17-23(40)15-34(32(6,7)42)26(17)27(47-31(41)22-12-10-9-11-13-22)29(45-19(3)37)33(8)24(44-18(2)36)14-25-35(16-43-25,48-21(5)39)28(33)30(34)46-20(4)38/h9-13,23-25,27-30,40,42H,14-16H2,1-8H3
SMILES:	CC1=C2C(C(C3(C)C(CC4C(CO4)(C3C(C2(CC1O)C(C)(C)O)OC(=O)C)OC(=O)C)OC(=O)C)OC(=O)C)OC(=O)c1ccccc1
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	5321662
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
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7264680]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	Roots	n.a.	n.a.	PMID[28581744]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	Stem Bark	n.a.	n.a.	PMID[28240909]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	needles	Himalayan	n.a.	PMID[16480866]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15125.2	Taxus wallichiana var. wallichiana	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15125.2	Taxus wallichiana var. wallichiana	Varieties	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO23720	Taxus wallichiana	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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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 NPC221895 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	301
0.1-0.2	1132
0.2-0.3	2375
0.3-0.4	5296
0.4-0.5	10393
0.5-0.6	11451
0.6-0.7	10406
0.7-0.8	1082
0.8-0.85	175
0.85-0.9	69
0.9-0.95	9
0.95-1	8

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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 NPC221895 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	245
0.1-0.2	739
0.2-0.3	1606
0.3-0.4	2835
0.4-0.5	2280
0.5-0.6	1156
0.6-0.7	272
0.7-0.8	17
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
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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