NPASS Compound

Structure

CID193765 OpenBabel06191715582D 64 67 0 0 1 0 0 0 0 0999 V2000 6.3383 2.4235 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0272 -1.1881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1871 -0.5448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9208 0.5261 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0063 0.8851 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9589 -3.0269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2907 -2.3067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8085 -1.1514 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8225 -4.0436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4532 2.8497 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6415 2.2963 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7149 1.3166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9032 0.7632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9766 -0.2165 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1649 -0.7699 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0565 -0.8071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6589 -0.3786 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2816 -1.4802 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0280 -3.1628 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6120 -2.5411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3209 -0.6771 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3993 -1.7493 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5441 -3.6099 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3304 -2.7625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0011 -0.5780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0767 -3.3148 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6589 -3.4448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2155 -0.6347 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2605 -1.5244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6405 -2.3947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1807 -0.7915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0011 -3.2455 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.3101 -1.3338 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5441 -0.2135 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0000 -3.8235 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0565 -3.0164 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3304 -1.0609 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5222 -3.0575 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2797 -0.3436 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2245 -1.7730 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3209 -2.4175 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5027 -2.2040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5829 -0.4708 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1527 -0.0864 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0011 -3.2455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1527 -3.7371 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5829 0.0437 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2889 0.3450 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1456 -1.9507 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7213 -3.9137 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1329 1.6157 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8656 -0.8585 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.2597 -2.1280 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.4741 -2.3504 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4600 -4.6702 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6015 1.0259 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1959 -1.9194 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1023 -3.3753 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4488 -2.0779 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6976 -2.1018 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5027 -1.6195 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4680 -0.8970 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5829 -3.8672 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 10 1 0 0 0 0 3 29 1 0 0 0 0 4 44 1 0 0 0 0 5 44 1 0 0 0 0 6 45 1 0 0 0 0 7 45 1 0 0 0 0 8 57 1 0 0 0 0 9 58 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 15 39 1 0 0 0 0 16 17 2 0 0 0 0 17 44 1 0 0 0 0 18 30 1 0 0 0 0 18 33 1 0 0 0 0 19 30 1 0 0 0 0 20 30 2 0 0 0 0 20 40 1 0 0 0 0 21 31 1 0 0 0 0 22 31 2 0 0 0 0 22 41 1 0 0 0 0 23 32 1 0 0 0 0 24 32 1 0 0 0 0 24 42 1 0 0 0 0 25 34 1 0 0 0 0 25 37 1 0 0 0 0 26 35 1 0 0 0 0 26 38 1 0 0 0 0 27 36 1 0 0 0 0 27 46 1 0 0 0 0 28 2 1 1 0 0 0 28 48 1 0 0 0 0 29 49 2 0 0 0 0 29 59 1 0 0 0 0 31 43 1 0 0 0 0 32 50 1 1 0 0 0 33 16 1 1 0 0 0 33 60 1 0 0 0 0 34 21 1 6 0 0 0 34 64 1 0 0 0 0 35 23 1 6 0 0 0 35 63 1 0 0 0 0 36 19 1 1 0 0 0 36 60 1 0 0 0 0 37 28 1 1 0 0 0 37 61 1 0 0 0 0 38 45 1 0 0 0 0 38 59 1 6 0 0 0 39 51 2 0 0 0 0 39 62 1 0 0 0 0 40 52 2 0 0 0 0 40 57 1 0 0 0 0 41 53 2 0 0 0 0 41 58 1 0 0 0 0 42 54 2 0 0 0 0 42 61 1 0 0 0 0 43 47 1 1 0 0 0 43 62 1 0 0 0 0 44 47 1 0 0 0 0 45 46 1 0 0 0 0 46 55 1 1 0 0 0 46 63 1 0 0 0 0 47 56 1 6 0 0 0 47 64 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	904.45
Volume:	910.311
LogP:	4.228
LogD:	2.459
LogS:	-5.247
# Rotatable Bonds:	15
TPSA:	240.11
# H-Bond Aceptor:	17
# H-Bond Donor:	4
# Rings:	4
# Heavy Atoms:	17

MedChem Properties

QED Drug-Likeness Score:	0.096
Synthetic Accessibility Score:	3.693
Fsp3:	0.681
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:	-5.225
MDCK Permeability:	0.00018022242875304073
Pgp-inhibitor:	0.219
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.114
20% Bioavailability (F20%):	0.838
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.074
Plasma Protein Binding (PPB):	75.47135162353516%
Volume Distribution (VD):	0.791
Pgp-substrate:	6.878053188323975%

ADMET: Metabolism

CYP1A2-inhibitor:	0.001
CYP1A2-substrate:	0.026
CYP2C19-inhibitor:	0.024
CYP2C19-substrate:	0.167
CYP2C9-inhibitor:	0.142
CYP2C9-substrate:	0.006
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.035
CYP3A4-inhibitor:	0.852
CYP3A4-substrate:	0.916

ADMET: Excretion

Clearance (CL):	1.926
Half-life (T1/2):	0.647

ADMET: Toxicity

hERG Blockers:	0.411
Human Hepatotoxicity (H-HT):	0.913
Drug-inuced Liver Injury (DILI):	0.964
AMES Toxicity:	0.644
Rat Oral Acute Toxicity:	0.245
Maximum Recommended Daily Dose:	1.0
Skin Sensitization:	0.969
Carcinogencity:	0.095
Eye Corrosion:	0.003
Eye Irritation:	0.016
Respiratory Toxicity:	0.943

Download Data

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

Natural Product: NPC193765

Natural Product ID:	NPC193765
*Common Name:**	Bryostatin
IUPAC Name:	n.a.
Synonyms:	Bryostatin; Bryostatin 1
Standard InCHIKey:	MJQUEDHRCUIRLF-TVIXENOKSA-N
Standard InCHI:	InChI=1S/C47H68O17/c1-10-11-12-13-14-15-39(51)62-43-31(22-41(53)58-9)21-34-25-37(28(2)48)61-42(54)24-32(50)23-35-26-38(59-29(3)49)45(6,7)46(55,63-35)27-36-19-30(20-40(52)57-8)18-33(60-36)16-17-44(4,5)47(43,56)64-34/h12-17,20,22,28,32-38,43,48,50,55-56H,10-11,18-19,21,23-27H2,1-9H3/b13-12+,15-14+,17-16+,30-20+,31-22+/t28-,32-,33+,34+,35-,36+,37-,38+,43+,46+,47-/m1/s1
SMILES:	CCC/C=C/C=C/C(=O)O[C@H]1/C(=C/C(=O)OC)/C[C@H]2C[C@H]([C@@H](C)O)OC(=O)C[C@@H](C[C@@H]3C[C@@H](C(C)(C)[C@@](C[C@@H]4C/C(=C/C(=O)OC)/C[C@H](/C=C/C(C)(C)[C@]1(O)O2)O4)(O)O3)OC(=O)C)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL449158
PubChem CID:	5280757
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0002995] Pentacarboxylic acids and derivatives

*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
NPO11979	Bugula neritina	Species	Bugulidae	Eukaryota	n.a.	n.a.	n.a.	PMID[8882431]
NPO11979	Bugula neritina	Species	Bugulidae	Eukaryota	n.a.	Gulf of Aomori, Japan	n.a.	PMID[8691208]
NPO11979	Bugula neritina	Species	Bugulidae	Eukaryota	n.a.	South China Sea	n.a.	PMID[25932671]
NPO11979	Bugula neritina	Species	Bugulidae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1021/ja00388a092]
NPO11979	Bugula neritina	Species	Bugulidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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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
EC50	2
GI50	6
IC50	662
Ki	4
Others	25
Potency	17

Activity Type	# Activity
Cell Line	672
CELL-LINE	1
Individual Protein	6
NON-MOLECULAR	5
ORGANISM	2
Others	30

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT153	Individual Protein	Androgen Receptor	Homo sapiens	Potency	n.a.	26832.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	14960.1	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	4.2	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	23914.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	10590.9	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	3.8	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	9439.2	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	2391.4	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	15089	nM	PubChem BioAssay data set
NPT2	Others	Unspecified		Potency	n.a.	4.7	nM	PubChem BioAssay data set

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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 NPC193765 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	227
0.1-0.2	1150
0.2-0.3	3730
0.3-0.4	6940
0.4-0.5	12959
0.5-0.6	10172
0.6-0.7	6018
0.7-0.8	1435
0.8-0.85	56
0.85-0.9	0
0.9-0.95	2
0.95-1	8

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Similarity Score	Similarity Level	Natural Product ID
0.96	High Similarity	NPC476738
0.96	High Similarity	NPC476740
0.9596	High Similarity	NPC473816
0.9596	High Similarity	NPC309398
0.9596	High Similarity	NPC474581

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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 NPC193765 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	200
0.1-0.2	1311
0.2-0.3	3377
0.3-0.4	2695
0.4-0.5	1020
0.5-0.6	407
0.6-0.7	114
0.7-0.8	25
0.8-0.85	1
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
0.8218	Intermediate Similarity	NPD7983	Approved
0.8095	Intermediate Similarity	NPD8029	Clinical (unspecified phase)
0.7949	Intermediate Similarity	NPD8515	Approved
0.7949	Intermediate Similarity	NPD8516	Approved
0.7949	Intermediate Similarity	NPD8513	Phase 3

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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