NPASS Compound

Structure

NPC471912 OpenBabel07101718182D 55 59 0 0 1 0 0 0 0 0999 V2000 2.4523 1.4702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0732 5.3547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7134 -2.2463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0398 1.6881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4835 -1.8453 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1438 -3.2258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0405 1.8140 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3459 -1.2290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0533 1.7193 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2948 2.1633 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0480 0.8404 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5310 1.7284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2842 0.4055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7620 0.4147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0035 0.8587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0495 2.9249 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3907 3.7348 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7820 0.0440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7155 0.1197 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1956 0.8569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4470 0.5913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2011 5.2453 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9496 -2.6812 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5090 2.3885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1521 -1.0313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4850 -2.4158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5257 0.8495 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6411 0.6610 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.7174 0.4330 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3874 -0.4508 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4432 -0.0354 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2397 0.4238 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1747 0.4363 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.9545 0.6592 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9499 -0.0973 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6366 -0.0954 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0709 0.9356 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7545 -0.4508 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1728 0.1229 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4164 0.1275 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3297 5.9457 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9444 -3.5601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.8502 3.1985 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6913 -0.3372 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3570 -2.3063 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7687 -1.2426 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2344 -0.4550 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2952 0.1196 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1401 4.4353 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4327 -1.7931 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6369 2.2791 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2814 -0.9113 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9542 -1.7153 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4812 0.8679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 21 2 0 0 0 0 2 22 1 0 0 0 0 3 23 1 0 0 0 0 4 24 1 0 0 0 0 5 25 1 0 0 0 0 6 26 1 0 0 0 0 7 37 1 0 0 0 0 8 38 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 27 2 0 0 0 0 13 27 1 0 0 0 0 14 15 2 0 0 0 0 14 27 1 0 0 0 0 15 32 1 0 0 0 0 16 17 1 0 0 0 0 17 49 1 0 0 0 0 18 28 1 0 0 0 0 18 30 1 0 0 0 0 19 29 1 0 0 0 0 19 31 1 0 0 0 0 20 37 1 0 0 0 0 20 50 1 0 0 0 0 21 29 1 0 0 0 0 21 33 1 0 0 0 0 22 41 2 0 0 0 0 22 49 1 0 0 0 0 23 42 2 0 0 0 0 23 51 1 0 0 0 0 24 43 2 0 0 0 0 24 52 1 0 0 0 0 25 44 2 0 0 0 0 25 53 1 0 0 0 0 26 45 2 0 0 0 0 26 54 1 0 0 0 0 28 34 1 0 0 0 0 28 37 1 6 0 0 0 29 55 1 1 0 0 0 30 38 1 0 0 0 0 30 46 2 0 0 0 0 31 39 1 6 0 0 0 31 51 1 0 0 0 0 32 47 2 0 0 0 0 32 55 1 0 0 0 0 33 34 1 0 0 0 0 33 39 1 6 0 0 0 34 52 1 1 0 0 0 35 36 1 0 0 0 0 35 39 1 1 0 0 0 35 53 1 0 0 0 0 36 40 1 6 0 0 0 36 54 1 0 0 0 0 37 40 1 6 0 0 0 38 40 1 6 0 0 0 38 50 1 0 0 0 0 39 16 1 6 0 0 0 40 48 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	768.3
Volume:	757.829
LogP:	2.382
LogD:	1.63
LogS:	-4.964
# Rotatable Bonds:	16
TPSA:	204.33
# H-Bond Aceptor:	15
# H-Bond Donor:	1
# Rings:	5
# Heavy Atoms:	15

MedChem Properties

QED Drug-Likeness Score:	0.157
Synthetic Accessibility Score:	6.624
Fsp3:	0.575
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:	-5.345
MDCK Permeability:	0.0001307719066971913
Pgp-inhibitor:	0.998
Pgp-substrate:	0.994
Human Intestinal Absorption (HIA):	0.815
20% Bioavailability (F20%):	0.843
30% Bioavailability (F30%):	0.997

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.534
Plasma Protein Binding (PPB):	50.282371520996094%
Volume Distribution (VD):	1.596
Pgp-substrate:	26.491283416748047%

ADMET: Metabolism

CYP1A2-inhibitor:	0.025
CYP1A2-substrate:	0.017
CYP2C19-inhibitor:	0.025
CYP2C19-substrate:	0.064
CYP2C9-inhibitor:	0.094
CYP2C9-substrate:	0.008
CYP2D6-inhibitor:	0.679
CYP2D6-substrate:	0.027
CYP3A4-inhibitor:	0.654
CYP3A4-substrate:	0.428

ADMET: Excretion

Clearance (CL):	2.976
Half-life (T1/2):	0.294

ADMET: Toxicity

hERG Blockers:	0.053
Human Hepatotoxicity (H-HT):	0.97
Drug-inuced Liver Injury (DILI):	0.947
AMES Toxicity:	0.063
Rat Oral Acute Toxicity:	0.561
Maximum Recommended Daily Dose:	0.746
Skin Sensitization:	0.359
Carcinogencity:	0.103
Eye Corrosion:	0.003
Eye Irritation:	0.013
Respiratory Toxicity:	0.965

Download Data

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

Natural Product: NPC471912

Natural Product ID:	NPC471912
*Common Name:**	AECANJMDROLQQG-OOIPFWLNSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	AECANJMDROLQQG-OOIPFWLNSA-N
Standard InCHI:	InChI=1S/C40H48O15/c1-21-29(55-32(47)15-14-27-12-10-9-11-13-27)19-31(51-23(3)42)39(16-17-49-22(2)41)33(21)34(52-24(4)43)28-18-30(46)38(8)40(48,37(28,7)20-50-38)36(54-26(6)45)35(39)53-25(5)44/h9-15,28-29,31,33-36,48H,1,16-20H2,2-8H3/b15-14+/t28-,29-,31-,33-,34+,35-,36-,37-,38+,39+,40-/m0/s1
SMILES:	CC(=O)OCCC12C(CC(C(=C)C1C(C3CC(=O)C4(C(C3(CO4)C)(C(C2OC(=O)C)OC(=O)C)O)C)OC(=O)C)OC(=O)C=CC5=CC=CC=C5)OC(=O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL329348
PubChem CID:	44327230
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0002967] Hexacarboxylic acids 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
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	wood	Yunnang Province, China	2000-OCT	PMID[21138310]
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	xylem	n.a.	PMID[21138310]
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]
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31343	Taxus chinensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29841	Taxus yunnanensis	Species	Taxaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO31343	Taxus chinensis	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

Activity Type	# Activity
ED50	3

Activity Type	# Activity
Cell Line	2
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1178	Cell Line	KB 3-1	Homo sapiens	ED50	=	17.0	ug ml-1	PMID[511796]
NPT1178	Cell Line	KB 3-1	Homo sapiens	ED50	=	4.6	ug ml-1	PMID[511796]
NPT27	Others	Unspecified	""	ED50	=	6.2	ug ml-1	PMID[511796]

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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 NPC471912 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	311
0.1-0.2	1046
0.2-0.3	2382
0.3-0.4	4823
0.4-0.5	8898
0.5-0.6	13960
0.6-0.7	9653
0.7-0.8	1310
0.8-0.85	269
0.85-0.9	32
0.9-0.95	8
0.95-1	5

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC80895
0.9926	High Similarity	NPC301946
0.9926	High Similarity	NPC277053
0.9375	High Similarity	NPC21410
0.9375	High Similarity	NPC473670

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 NPC471912 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	252
0.1-0.2	713
0.2-0.3	1622
0.3-0.4	3201
0.4-0.5	2126
0.5-0.6	927
0.6-0.7	290
0.7-0.8	18
0.8-0.85	1
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
0.831	Intermediate Similarity	NPD7966	Clinical (unspecified phase)
0.8121	Intermediate Similarity	NPD8407	Phase 2
0.8049	Intermediate Similarity	NPD8368	Discontinued
0.7917	Intermediate Similarity	NPD8434	Phase 2
0.7914	Intermediate Similarity	NPD7799	Discontinued

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