NPASS Compound

Structure

NPC470208 OpenBabel07101719252D 46 52 0 0 1 0 0 0 0 0999 V2000 -2.8960 7.2842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7417 3.8545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3773 1.7308 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7446 5.8143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8931 5.3243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6403 2.8117 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1987 8.2641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7417 1.8946 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5070 0.0003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4170 -1.2014 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0474 3.8545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0474 6.7942 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8931 3.3645 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5677 1.1787 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8960 5.3243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0444 4.8344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1693 2.2597 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1987 7.2842 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.8931 2.3846 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6241 0.4255 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8960 4.3444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1987 4.3444 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0474 5.8143 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0444 3.8545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1129 1.5065 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1987 5.3243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7370 1.0810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1958 3.3645 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3472 4.8344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4740 2.1620 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1958 5.3243 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4175 1.4087 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8499 2.5875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3501 5.8143 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1958 2.3846 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3472 3.8545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6806 0.3277 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 -3.7446 3.8545 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3501 3.8545 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1958 6.3043 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2272 0.8567 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4902 -0.2243 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3501 6.7942 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0444 1.8946 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 0.7934 3.3407 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4 15 1 0 0 0 0 5 16 1 0 0 0 0 6 17 1 0 0 0 0 10 42 1 0 0 0 0 11 21 2 0 0 0 0 11 22 1 0 0 0 0 12 1 1 6 0 0 0 12 18 1 0 0 0 0 12 23 1 0 0 0 0 13 2 1 6 0 0 0 13 19 1 0 0 0 0 13 24 1 0 0 0 0 14 3 1 1 0 0 0 14 20 1 0 0 0 0 14 25 1 0 0 0 0 15 21 1 0 0 0 0 15 23 2 0 0 0 0 16 24 2 0 0 0 0 16 31 1 0 0 0 0 17 25 2 0 0 0 0 17 33 1 0 0 0 0 18 7 1 1 0 0 0 18 43 1 0 0 0 0 19 8 1 1 0 0 0 19 44 1 0 0 0 0 20 9 1 6 0 0 0 20 45 1 0 0 0 0 21 38 1 0 0 0 0 22 26 2 0 0 0 0 22 39 1 0 0 0 0 23 26 1 0 0 0 0 24 28 1 0 0 0 0 25 27 1 0 0 0 0 26 34 1 0 0 0 0 27 32 2 0 0 0 0 27 37 1 0 0 0 0 28 36 2 0 0 0 0 29 31 2 0 0 0 0 29 36 1 0 0 0 0 30 32 1 0 0 0 0 30 33 2 0 0 0 0 30 35 1 0 0 0 0 31 40 1 0 0 0 0 32 41 1 0 0 0 0 33 46 1 0 0 0 0 34 29 1 6 0 0 0 34 43 1 0 0 0 0 35 28 1 1 0 0 0 35 44 1 0 0 0 0 36 46 1 0 0 0 0 37 42 1 0 0 0 0 37 45 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	632.3
Volume:	643.997
LogP:	7.59
LogD:	3.64
LogS:	-4.556
# Rotatable Bonds:	2
TPSA:	127.07
# H-Bond Aceptor:	9
# H-Bond Donor:	4
# Rings:	7
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.223
Synthetic Accessibility Score:	5.859
Fsp3:	0.514
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:	-5.926
MDCK Permeability:	1.822405101847835e-05
Pgp-inhibitor:	0.902
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.689
20% Bioavailability (F20%):	0.421
30% Bioavailability (F30%):	0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.006
Plasma Protein Binding (PPB):	99.92951202392578%
Volume Distribution (VD):	0.548
Pgp-substrate:	3.071277141571045%

ADMET: Metabolism

CYP1A2-inhibitor:	0.006
CYP1A2-substrate:	0.959
CYP2C19-inhibitor:	0.065
CYP2C19-substrate:	0.956
CYP2C9-inhibitor:	0.097
CYP2C9-substrate:	0.935
CYP2D6-inhibitor:	0.017
CYP2D6-substrate:	0.116
CYP3A4-inhibitor:	0.093
CYP3A4-substrate:	0.915

ADMET: Excretion

Clearance (CL):	1.527
Half-life (T1/2):	0.037

ADMET: Toxicity

hERG Blockers:	0.062
Human Hepatotoxicity (H-HT):	0.21
Drug-inuced Liver Injury (DILI):	0.941
AMES Toxicity:	0.083
Rat Oral Acute Toxicity:	0.998
Maximum Recommended Daily Dose:	0.999
Skin Sensitization:	0.912
Carcinogencity:	0.039
Eye Corrosion:	0.003
Eye Irritation:	0.901
Respiratory Toxicity:	0.403

Download Data

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

Natural Product: NPC470208

Natural Product ID:	NPC470208
*Common Name:**	Tricitrinol B
IUPAC Name:	n.a.
Synonyms:	Tricitrinol B
Standard InCHIKey:	GIHKMCLRUJERAC-ITWOFJKESA-N
Standard InCHI:	InChI=1S/C37H44O9/c1-12-18(7)43-34(26-22(39)11-21(38)15(4)23(12)26)29-31(40)16(5)24-13(2)19(8)44-35-28(24)36(29)46-33-17(6)25-14(3)20(9)45-37(42-10)27(25)32(41)30(33)35/h11-14,18-20,34-35,37-41H,1-10H3/t12-,13-,14-,18-,19-,20-,34+,35-,37?/m1/s1
SMILES:	COC1O[C@H](C)[C@H](c2c1c(O)c1[C@@H]3O[C@H](C)[C@H](c4c3c(Oc1c2C)c(c(c4C)O)[C@H]1O[C@H](C)[C@H](c2c1c(O)cc(c2C)O)C)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1822982
PubChem CID:	46840960
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes

*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
NPO33186	penicillium citrinum hgy1-5	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21761866]

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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	22
Others	22

Activity Type	# Activity
Cell Line	42
NON-MOLECULAR	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT116	Cell Line	HL-60	Homo sapiens	IC50	=	3200.0	nM	PMID[536931]
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	=	4820.0	nM	PMID[536931]
NPT91	Cell Line	KB	Homo sapiens	IC50	=	3870.0	nM	PMID[536931]
NPT1081	Cell Line	BXPC-3	Homo sapiens	IC50	=	4830.0	nM	PMID[536931]
NPT393	Cell Line	HCT-116	Homo sapiens	IC50	=	4830.0	nM	PMID[536931]
NPT181	Cell Line	Bel-7402	Homo sapiens	IC50	=	4830.0	nM	PMID[536931]
NPT1097	Cell Line	MKN-45	Homo sapiens	IC50	=	4830.0	nM	PMID[536931]
NPT515	Cell Line	SGC-7901	Homo sapiens	IC50	=	4830.0	nM	PMID[536931]
NPT306	Cell Line	PC-3	Homo sapiens	IC50	=	4830.0	nM	PMID[536931]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	4830.0	nM	PMID[536931]

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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 NPC470208 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	443
0.1-0.2	1724
0.2-0.3	4147
0.3-0.4	10721
0.4-0.5	8065
0.5-0.6	4521
0.6-0.7	8266
0.7-0.8	4200
0.8-0.85	509
0.85-0.9	94
0.9-0.95	3
0.95-1	4

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC295573
0.8936	High Similarity	NPC24913
0.8936	High Similarity	NPC177712
0.8933	High Similarity	NPC259707
0.8774	High Similarity	NPC185231

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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 NPC470208 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	373
0.1-0.2	998
0.2-0.3	1872
0.3-0.4	2782
0.4-0.5	1607
0.5-0.6	946
0.6-0.7	483
0.7-0.8	84
0.8-0.85	4
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8462	Intermediate Similarity	NPD4907	Clinical (unspecified phase)
0.8322	Intermediate Similarity	NPD4908	Phase 1
0.8146	Intermediate Similarity	NPD6674	Discontinued
0.8138	Intermediate Similarity	NPD4625	Phase 3
0.7975	Intermediate Similarity	NPD6959	Discontinued

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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