NPASS Compound

Structure

NPC156851 OpenBabel06302216212D 42 46 0 0 1 0 0 0 0 0999 V2000 -4.3301 1.5000 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 -5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 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 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 5.0000 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 -0.0000 2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 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 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 42 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 12 11 1 6 0 0 0 12 13 1 0 0 0 0 12 19 1 0 0 0 0 13 14 1 1 0 0 0 13 16 1 0 0 0 0 14 15 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 22 1 1 0 0 0 18 19 1 0 0 0 0 18 21 1 6 0 0 0 19 20 1 1 0 0 0 22 23 1 0 0 0 0 23 40 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 25 41 1 0 0 0 0 26 39 2 0 0 0 0 26 27 1 0 0 0 0 27 28 2 0 0 0 0 27 29 1 0 0 0 0 29 30 2 0 0 0 0 30 31 1 0 0 0 0 30 38 1 0 0 0 0 31 36 2 0 0 0 0 31 32 1 0 0 0 0 32 33 2 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 34 37 1 0 0 0 0 35 36 1 0 0 0 0 38 39 1 0 0 0 0 39 40 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	578.14
Volume:	555.862
LogP:	3.549
LogD:	2.529
LogS:	-4.497
# Rotatable Bonds:	8
TPSA:	196.35
# H-Bond Aceptor:	12
# H-Bond Donor:	6
# Rings:	5
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.138
Synthetic Accessibility Score:	4.127
Fsp3:	0.2
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:	-6.296
MDCK Permeability:	1.5503990653087385e-05
Pgp-inhibitor:	0.015
Pgp-substrate:	0.866
Human Intestinal Absorption (HIA):	0.549
20% Bioavailability (F20%):	0.693
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.011
Plasma Protein Binding (PPB):	100.44757843017578%
Volume Distribution (VD):	0.64
Pgp-substrate:	2.3091769218444824%

ADMET: Metabolism

CYP1A2-inhibitor:	0.655
CYP1A2-substrate:	0.024
CYP2C19-inhibitor:	0.306
CYP2C19-substrate:	0.052
CYP2C9-inhibitor:	0.548
CYP2C9-substrate:	0.866
CYP2D6-inhibitor:	0.781
CYP2D6-substrate:	0.309
CYP3A4-inhibitor:	0.461
CYP3A4-substrate:	0.082

ADMET: Excretion

Clearance (CL):	3.816
Half-life (T1/2):	0.574

ADMET: Toxicity

hERG Blockers:	0.352
Human Hepatotoxicity (H-HT):	0.421
Drug-inuced Liver Injury (DILI):	0.95
AMES Toxicity:	0.656
Rat Oral Acute Toxicity:	0.03
Maximum Recommended Daily Dose:	0.053
Skin Sensitization:	0.951
Carcinogencity:	0.088
Eye Corrosion:	0.003
Eye Irritation:	0.043
Respiratory Toxicity:	0.035

Download Data

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

Natural Product: NPC156851

Natural Product ID:	NPC156851
*Common Name:**	UTUISHMYVAZILQ-NBJODKRESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	UTUISHMYVAZILQ-NBJODKRESA-N
Standard InCHI:	InChI=1S/C30H26O12/c31-14-24-29(42-25(36)10-3-15-1-6-17(32)7-2-15)27(37)28(38)30(41-24)39-19-11-20(34)26-21(35)13-22(40-23(26)12-19)16-4-8-18(33)9-5-16/h1-13,24,27-34,37-38H,14H2/b10-3-/t24-,27-,28-,29-,30-/m1/s1
SMILES:	c1cc(ccc1/C=CC(=O)O[C@@H]1[C@@H](CO)O[C@H]([C@@H]([C@H]1O)O)Oc1cc(c2c(=O)cc(c3ccc(cc3)O)oc2c1)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	16109840
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-O-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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO2804	Calophyllum inophyllum	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15678383]
NPO2804	Calophyllum inophyllum	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16045947]
NPO8764	Laurencia decumbens	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17711344]
NPO8653	Leuconostoc mesenteroides	Species	Leuconostocaceae	Bacteria	n.a.	n.a.	n.a.	PMID[19025748]
NPO24671	Lycopodium japonicum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19245240]
NPO2804	Calophyllum inophyllum	Species	Calophyllaceae	Eukaryota	n.a.	stem	n.a.	PMID[20188156]
NPO3123	Anthemis cretica	Species	Asteraceae	Eukaryota	n.a.	aerial part	n.a.	PMID[22351977]
NPO2804	Calophyllum inophyllum	Species	Calophyllaceae	Eukaryota	n.a.	Malaysian	n.a.	PMID[7506311]
NPO24671	Lycopodium japonicum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO2804	Calophyllum inophyllum	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3123	Anthemis cretica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24671	Lycopodium japonicum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO2804	Calophyllum inophyllum	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28741	Afrocarpus gracilior	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24671	Lycopodium japonicum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6766	Antiphiona pinnatisecta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9567	Enicosanthum cupulare	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8653	Leuconostoc mesenteroides	Species	Leuconostocaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO2804	Calophyllum inophyllum	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10991	Maackia tashiroi	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8764	Laurencia decumbens	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2012	Turnera diffusa	Species	Passifloraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9136	Pseudocyclosorus subochthodes	Species	Thelypteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24671	Lycopodium japonicum	Species	Lycopodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28741	Afrocarpus gracilior	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3123	Anthemis cretica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2495	Agave xylonacantha	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19826	Helicoverpa armigera	Species	0ctuidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26103	Streptomyces bobili	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ 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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC156851 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	395
0.1-0.2	1617
0.2-0.3	3881
0.3-0.4	8714
0.4-0.5	9691
0.5-0.6	4629
0.6-0.7	5749
0.7-0.8	5296
0.8-0.85	1705
0.85-0.9	696
0.9-0.95	270
0.95-1	54

Similarity Score	Similarity Level	Natural Product ID

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 NPC156851 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	356
0.1-0.2	905
0.2-0.3	1795
0.3-0.4	2677
0.4-0.5	1957
0.5-0.6	994
0.6-0.7	286
0.7-0.8	130
0.8-0.85	33
0.85-0.9	16
0.9-0.95	1
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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