NPASS Compound

Structure

CID195954 OpenBabel06191715582D 34 37 0 0 1 0 0 0 0 0999 V2000 -2.5981 -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 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -0.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 0.5000 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 -4.4152 -1.3090 0.0000 C 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 -5.0029 -0.5000 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 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 3.5000 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 -1.7321 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 1 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 0.0000 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 -0.8660 1.5000 0.0000 C 0 0 1 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 -0.8660 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 4.5000 0.0000 O 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 0.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4152 0.3090 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 -1.7321 2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 13 2 0 0 0 0 2 14 1 0 0 0 0 3 15 1 0 0 0 0 4 16 1 0 0 0 0 5 24 1 0 0 0 0 6 24 1 0 0 0 0 7 25 1 0 0 0 0 8 10 1 0 0 0 0 9 11 2 0 0 0 0 9 18 1 0 0 0 0 10 26 1 0 0 0 0 11 31 1 0 0 0 0 12 19 1 0 0 0 0 12 20 1 0 0 0 0 13 17 1 0 0 0 0 13 18 1 0 0 0 0 14 27 2 0 0 0 0 14 32 1 0 0 0 0 15 28 2 0 0 0 0 15 33 1 0 0 0 0 16 29 2 0 0 0 0 16 34 1 0 0 0 0 17 8 1 1 0 0 0 17 19 1 0 0 0 0 18 20 2 0 0 0 0 19 25 1 6 0 0 0 20 31 1 0 0 0 0 21 22 1 0 0 0 0 21 23 1 0 0 0 0 21 32 1 1 0 0 0 22 24 1 0 0 0 0 22 33 1 1 0 0 0 23 25 1 1 0 0 0 23 34 1 0 0 0 0 24 26 1 0 0 0 0 25 26 1 6 0 0 0 26 30 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	474.23
Volume:	478.529
LogP:	3.24
LogD:	2.591
LogS:	-4.301
# Rotatable Bonds:	6
TPSA:	112.27
# H-Bond Aceptor:	8
# H-Bond Donor:	1
# Rings:	4
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.524
Synthetic Accessibility Score:	5.021
Fsp3:	0.654
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.089
MDCK Permeability:	3.0000072001712397e-05
Pgp-inhibitor:	0.995
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.388
20% Bioavailability (F20%):	0.819
30% Bioavailability (F30%):	0.958

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.246
Plasma Protein Binding (PPB):	78.69375610351562%
Volume Distribution (VD):	2.391
Pgp-substrate:	22.32061004638672%

ADMET: Metabolism

CYP1A2-inhibitor:	0.292
CYP1A2-substrate:	0.043
CYP2C19-inhibitor:	0.099
CYP2C19-substrate:	0.089
CYP2C9-inhibitor:	0.342
CYP2C9-substrate:	0.044
CYP2D6-inhibitor:	0.916
CYP2D6-substrate:	0.158
CYP3A4-inhibitor:	0.663
CYP3A4-substrate:	0.374

ADMET: Excretion

Clearance (CL):	3.025
Half-life (T1/2):	0.355

ADMET: Toxicity

hERG Blockers:	0.831
Human Hepatotoxicity (H-HT):	0.737
Drug-inuced Liver Injury (DILI):	0.842
AMES Toxicity:	0.053
Rat Oral Acute Toxicity:	0.854
Maximum Recommended Daily Dose:	0.254
Skin Sensitization:	0.274
Carcinogencity:	0.175
Eye Corrosion:	0.005
Eye Irritation:	0.01
Respiratory Toxicity:	0.975

Download Data

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

Natural Product: NPC195954

Natural Product ID:	NPC195954
*Common Name:**	14(17)-Dehydrocaesalpin F
IUPAC Name:	[(1R,2S,3S,4aR,6aR,11aS,11bS)-1,3-diacetyloxy-4a-hydroxy-4,4,11b-trimethyl-7-methylidene-1,2,3,5,6,6a,11,11a-octahydronaphtho[2,1-f][1]benzofuran-2-yl] acetate
Synonyms:	14(17)-Dehydrocaesalpin F
Standard InCHIKey:	PPFRBUXKYCVYTK-GIPIGPSXSA-N
Standard InCHI:	InChI=1S/C26H34O8/c1-13-17-8-10-26(30)24(5,6)22(33-15(3)28)21(32-14(2)27)23(34-16(4)29)25(26,7)19(17)12-20-18(13)9-11-31-20/h9,11,17,19,21-23,30H,1,8,10,12H2,2-7H3/t17-,19-,21-,22+,23-,25-,26+/m0/s1
SMILES:	C=C1[C@@H]2CC[C@]3(C(C)(C)[C@@H]([C@@H]([C@@H]([C@]3(C)[C@H]2Cc2c1cco2)OC(=O)C)OC(=O)C)OC(=O)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL517030
PubChem CID:	44584000
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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
NPO25179	Guilandina bonduc	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26756595]
NPO26402	Caesalpinia crista	Species	Fabaceae	Eukaryota	n.a.	Indonesia	n.a.	PMID[15921414]
NPO26402	Caesalpinia crista	Species	Fabaceae	Eukaryota	n.a.	seed kernel	n.a.	PMID[15921414]
NPO11853	Eucalyptus froggattii	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7886	Eria tomentosa	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13248	Pistacia mexicana	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25179	Guilandina bonduc	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26402	Caesalpinia crista	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26402	Caesalpinia crista	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]

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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
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	200.0	nM	PMID[536378]

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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 NPC195954 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	332
0.1-0.2	1268
0.2-0.3	2605
0.3-0.4	5033
0.4-0.5	9898
0.5-0.6	8539
0.6-0.7	7106
0.7-0.8	7190
0.8-0.85	512
0.85-0.9	153
0.9-0.95	53
0.95-1	8

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Similarity Score	Similarity Level	Natural Product ID
0.9866	High Similarity	NPC88007
0.9733	High Similarity	NPC194499
0.9671	High Similarity	NPC68848
0.9595	High Similarity	NPC212257
0.9542	High Similarity	NPC188649

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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 NPC195954 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	287
0.1-0.2	813
0.2-0.3	1598
0.3-0.4	2514
0.4-0.5	2156
0.5-0.6	1195
0.6-0.7	460
0.7-0.8	121
0.8-0.85	6
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
0.8802	High Similarity	NPD8434	Phase 2
0.8261	Intermediate Similarity	NPD5760	Phase 2
0.8261	Intermediate Similarity	NPD5761	Phase 2
0.8176	Intermediate Similarity	NPD6765	Approved
0.8176	Intermediate Similarity	NPD6764	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