NPASS Compound

Structure

NPC58350 OpenBabel06302215422D 69 77 0 0 1 0 0 0 0 0999 V2000 -4.7150 -0.9121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7150 -0.9121 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2150 -0.0461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2150 -0.0461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7150 0.8199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2150 1.6859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2150 1.6859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7150 0.8199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7150 0.8199 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7150 2.5520 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2150 3.4180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7150 0.8199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2150 -0.0461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7850 -0.0461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2850 -0.9121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2850 -0.9121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7850 -1.7782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2850 -2.6442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7850 -3.5102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7850 -3.5102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2850 -2.6442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2850 -2.6442 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7850 -1.7782 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.2850 -0.9121 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.7850 -0.0461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7850 -0.0461 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2850 0.8199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7850 1.6859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7850 1.6859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2850 0.8199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2850 2.5520 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.2850 2.5520 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2850 -0.9121 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7850 -1.7782 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7850 -1.7782 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2850 -4.3763 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2850 -2.6442 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7850 -0.0461 0.0000 O 0 3 0 0 0 0 0 0 0 0 0 0 2.2850 0.8199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5122 1.5565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0779 2.1934 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3093 2.2510 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7850 1.6859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2850 0.8199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2150 1.6859 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5779 3.0594 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8557 -1.4821 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8557 -0.4940 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7114 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7114 0.9881 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8557 1.4821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 0.9881 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8557 1.4821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7114 0.9881 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5671 1.4821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4229 0.9881 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5671 2.4702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4229 2.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2786 2.4702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1343 2.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9900 2.4702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9900 1.4821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1343 0.9881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2786 1.4821 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8457 0.9881 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 -0.8557 2.4702 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5671 1.4821 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5671 -0.4940 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 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 12 1 0 0 0 0 6 7 2 0 0 0 0 7 8 1 0 0 0 0 7 10 1 0 0 0 0 8 9 1 0 0 0 0 10 11 1 0 0 0 0 12 45 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 13 47 1 0 0 0 0 14 44 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 16 38 1 0 0 0 0 17 34 2 0 0 0 0 17 18 1 0 0 0 0 18 19 2 0 0 0 0 18 37 1 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 36 1 0 0 0 0 21 34 1 0 0 0 0 21 22 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 23 35 1 1 0 0 0 24 25 1 6 0 0 0 24 33 1 0 0 0 0 25 30 2 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 28 32 1 0 0 0 0 29 30 1 0 0 0 0 29 31 1 0 0 0 0 33 34 1 0 0 0 0 38 39 2 0 0 0 0 39 44 1 0 0 0 0 39 40 1 0 0 0 0 40 41 2 0 0 0 0 41 42 1 0 0 0 0 41 46 1 0 0 0 0 42 43 2 0 0 0 0 43 44 1 0 0 0 0 43 45 1 0 0 0 0 48 47 1 1 0 0 0 48 49 1 0 0 0 0 48 66 1 0 0 0 0 49 50 1 0 0 0 0 49 69 1 6 0 0 0 50 51 1 0 0 0 0 50 68 1 1 0 0 0 51 52 1 0 0 0 0 51 67 1 6 0 0 0 52 53 1 1 0 0 0 52 66 1 0 0 0 0 53 54 1 0 0 0 0 54 55 1 0 0 0 0 55 56 2 0 0 0 0 55 57 1 0 0 0 0 57 58 2 3 0 0 0 58 59 1 0 0 0 0 59 64 2 0 0 0 0 59 60 1 0 0 0 0 60 61 2 0 0 0 0 61 62 1 0 0 0 0 62 63 2 0 0 0 0 62 65 1 0 0 0 0 63 64 1 0 0 0 0 M CHG 1 38 1 M END $$$$

Physi-Chem Properties

Molecular Weight:	951.23
Volume:	903.445
LogP:	5.118
LogD:	2.349
LogS:	-4.182
# Rotatable Bonds:	12
TPSA:	317.76
# H-Bond Aceptor:	20
# H-Bond Donor:	11
# Rings:	9
# Heavy Atoms:	20

MedChem Properties

QED Drug-Likeness Score:	0.036
Synthetic Accessibility Score:	5.794
Fsp3:	0.224
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.63
MDCK Permeability:	9.133236744673923e-06
Pgp-inhibitor:	0.728
Pgp-substrate:	0.988
Human Intestinal Absorption (HIA):	0.803
20% Bioavailability (F20%):	0.064
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001
Plasma Protein Binding (PPB):	88.99945068359375%
Volume Distribution (VD):	0.36
Pgp-substrate:	29.116111755371094%

ADMET: Metabolism

CYP1A2-inhibitor:	0.061
CYP1A2-substrate:	0.118
CYP2C19-inhibitor:	0.039
CYP2C19-substrate:	0.041
CYP2C9-inhibitor:	0.553
CYP2C9-substrate:	0.386
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.204
CYP3A4-inhibitor:	0.069
CYP3A4-substrate:	0.047

ADMET: Excretion

Clearance (CL):	5.424
Half-life (T1/2):	0.708

ADMET: Toxicity

hERG Blockers:	0.162
Human Hepatotoxicity (H-HT):	0.168
Drug-inuced Liver Injury (DILI):	0.978
AMES Toxicity:	0.675
Rat Oral Acute Toxicity:	0.082
Maximum Recommended Daily Dose:	0.842
Skin Sensitization:	0.954
Carcinogencity:	0.04
Eye Corrosion:	0.003
Eye Irritation:	0.812
Respiratory Toxicity:	0.009

Download Data

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

Natural Product: NPC58350

Natural Product ID:	NPC58350
*Common Name:**	KIRBPGMHGPWCPX-DKVHZQDTSA-O
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KIRBPGMHGPWCPX-DKVHZQDTSA-O
Standard InCHI:	InChI=1S/C49H42O20/c1-62-35-12-22(13-36(63-2)41(35)58)46-48(69-49-44(61)43(60)42(59)37(67-49)19-64-38(57)10-5-20-3-7-23(50)8-4-20)26-17-34(65-32-14-24(51)15-33(66-46)39(26)32)40-30(55)18-28(53)25-16-31(56)45(68-47(25)40)21-6-9-27(52)29(54)11-21/h3-15,17-18,31,37,42-45,49,56,59-61H,16,19H2,1-2H3,(H6-,50,51,52,53,54,55,57,58)/p+1/t31-,37+,42+,43-,44+,45+,49-/m0/s1
SMILES:	COc1cc(cc(c1O)OC)C1=C(c2cc(c3c(cc(c4C[C@@H]([C@@H](c5ccc(c(c5)O)O)Oc34)O)O)O)[o+]c3cc(cc(c23)O1)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](COC(=O)C=Cc2ccc(cc2)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	102051215
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003678] Flavonoid 3-O-p-coumaroyl 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
NPO14685	Swertia franchetiana	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7561895]
NPO14685	Swertia franchetiana	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7513747]
NPO13847	Streptomyces avermectinius	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[464561]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31433178]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Seeds	Benedictine Pannonhalma Archabbey, Hungary		PMID[29803478]
NPO26327	Chaenomeles sinensis	Species	Rosaceae	Eukaryota	Twigs	n.a.	n.a.	PMID[28358502]
NPO26327	Chaenomeles sinensis	Species	Rosaceae	Eukaryota	Twigs	n.a.	n.a.	PMID[25894905]
NPO13847	Streptomyces avermectinius	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[25611131]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	Stalks	n.a.	n.a.	PMID[24521157]
NPO17024	Vitis vinifera	Species	Vitaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23759170]

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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 NPC58350 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	436
0.1-0.2	1838
0.2-0.3	3908
0.3-0.4	9186
0.4-0.5	8895
0.5-0.6	4788
0.6-0.7	5511
0.7-0.8	5571
0.8-0.85	1564
0.85-0.9	701
0.9-0.95	299
0.95-1	0

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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 NPC58350 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	393
0.1-0.2	963
0.2-0.3	1967
0.3-0.4	2696
0.4-0.5	1869
0.5-0.6	850
0.6-0.7	266
0.7-0.8	110
0.8-0.85	24
0.85-0.9	6
0.9-0.95	6
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