NPASS Compound

Structure

CID115466 OpenBabel06191715472D 37 40 0 0 1 0 0 0 0 0999 V2000 7.0756 -6.8823 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6504 -3.6389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3936 -4.3080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9562 -3.2788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4915 -4.9260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3871 -3.5878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6994 -3.9479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.0052 -3.5878 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 9.1857 -5.2862 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2346 -5.5952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0000 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.6962 -4.5388 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.9288 -5.9553 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2839 -5.3479 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.0267 -6.5733 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6962 -4.5388 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 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 1 33 1 0 0 0 0 2 34 1 0 0 0 0 3 5 2 0 0 0 0 3 14 1 0 0 0 0 4 6 2 0 0 0 0 4 13 1 0 0 0 0 5 17 1 0 0 0 0 6 18 1 0 0 0 0 7 13 1 0 0 0 0 8 14 1 0 0 0 0 9 14 2 0 0 0 0 9 19 1 0 0 0 0 10 13 2 0 0 0 0 10 20 1 0 0 0 0 11 27 1 0 0 0 0 12 15 1 0 0 0 0 12 35 1 0 0 0 0 15 7 1 1 0 0 0 15 16 1 0 0 0 0 16 8 1 6 0 0 0 16 25 1 0 0 0 0 17 19 2 0 0 0 0 17 28 1 0 0 0 0 18 20 2 0 0 0 0 18 36 1 0 0 0 0 19 33 1 0 0 0 0 20 34 1 0 0 0 0 21 11 1 1 0 0 0 21 22 1 0 0 0 0 21 37 1 0 0 0 0 22 23 1 0 0 0 0 22 29 1 6 0 0 0 23 24 1 0 0 0 0 23 30 1 1 0 0 0 24 26 1 0 0 0 0 24 31 1 6 0 0 0 25 32 2 0 0 0 0 25 35 1 0 0 0 0 26 36 1 1 0 0 0 26 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	520.19
Volume:	502.264
LogP:	1.061
LogD:	1.226
LogS:	-3.466
# Rotatable Bonds:	9
TPSA:	164.37
# H-Bond Aceptor:	11
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.286
Synthetic Accessibility Score:	4.166
Fsp3:	0.5
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.093
MDCK Permeability:	2.32374277402414e-05
Pgp-inhibitor:	0.03
Pgp-substrate:	0.221
Human Intestinal Absorption (HIA):	0.243
20% Bioavailability (F20%):	0.006
30% Bioavailability (F30%):	0.801

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.186
Plasma Protein Binding (PPB):	80.9142837524414%
Volume Distribution (VD):	0.334
Pgp-substrate:	13.95608139038086%

ADMET: Metabolism

CYP1A2-inhibitor:	0.069
CYP1A2-substrate:	0.299
CYP2C19-inhibitor:	0.048
CYP2C19-substrate:	0.794
CYP2C9-inhibitor:	0.027
CYP2C9-substrate:	0.556
CYP2D6-inhibitor:	0.137
CYP2D6-substrate:	0.829
CYP3A4-inhibitor:	0.386
CYP3A4-substrate:	0.232

ADMET: Excretion

Clearance (CL):	11.19
Half-life (T1/2):	0.837

ADMET: Toxicity

hERG Blockers:	0.412
Human Hepatotoxicity (H-HT):	0.267
Drug-inuced Liver Injury (DILI):	0.135
AMES Toxicity:	0.119
Rat Oral Acute Toxicity:	0.009
Maximum Recommended Daily Dose:	0.063
Skin Sensitization:	0.667
Carcinogencity:	0.292
Eye Corrosion:	0.003
Eye Irritation:	0.02
Respiratory Toxicity:	0.022

Download Data

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

Natural Product: NPC115466

Natural Product ID:	NPC115466
*Common Name:**	Styraxlignolide D
IUPAC Name:	(3S,4S)-3-[(4-hydroxy-3-methoxyphenyl)methyl]-4-[[3-methoxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]methyl]oxolan-2-one
Synonyms:	Styraxlignolide D
Standard InCHIKey:	FWRZDNFXFFWBGP-ZQJJHTFWSA-N
Standard InCHI:	InChI=1S/C26H32O11/c1-33-19-9-14(3-5-17(19)28)8-16-15(12-35-25(16)32)7-13-4-6-18(20(10-13)34-2)36-26-24(31)23(30)22(29)21(11-27)37-26/h3-6,9-10,15-16,21-24,26-31H,7-8,11-12H2,1-2H3/t15-,16+,21-,22-,23+,24-,26-/m1/s1
SMILES:	COc1cc(ccc1O)C[C@H]1[C@H](Cc2ccc(c(c2)OC)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)COC1=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL519055
PubChem CID:	11179934
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001511] Lignan glycosides

*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
NPO30866	Styrax japonica	Species	Styracaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[15620237]
NPO30866	Styrax japonica	Species	Styracaceae	Eukaryota	n.a.	bark	n.a.	PMID[15577246]
NPO17951	Styrax japonicus	Species	Styracaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17951	Styrax japonicus	Species	Styracaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO30866	Styrax japonica	Species	Styracaceae	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
IC50	1

Activity Type	# Activity
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1	Others	Radical scavenging activity		IC50	=	278000.0	nM	PMID[495501]

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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 NPC115466 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	314
0.1-0.2	1221
0.2-0.3	2881
0.3-0.4	6414
0.4-0.5	10764
0.5-0.6	6377
0.6-0.7	7790
0.7-0.8	5852
0.8-0.85	811
0.85-0.9	244
0.9-0.95	16
0.95-1	13

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC245615
1.0	High Similarity	NPC299706
1.0	High Similarity	NPC61604
0.9797	High Similarity	NPC163635
0.9793	High Similarity	NPC229882

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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 NPC115466 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	262
0.1-0.2	736
0.2-0.3	1634
0.3-0.4	2529
0.4-0.5	2152
0.5-0.6	1136
0.6-0.7	595
0.7-0.8	95
0.8-0.85	6
0.85-0.9	5
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8875	High Similarity	NPD7228	Approved
0.879	High Similarity	NPD6234	Discontinued
0.871	High Similarity	NPD37	Approved
0.8662	High Similarity	NPD4967	Phase 2
0.8662	High Similarity	NPD4965	Approved

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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