NPASS Compound

Structure

NPC288350 OpenBabel07101718192D 44 45 0 0 1 0 0 0 0 0999 V2000 0.3902 -1.9616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0890 -1.6237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9685 4.5567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6841 -1.9002 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4835 2.2894 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.9515 -0.3852 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6457 0.0165 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1731 3.2363 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5330 2.6796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0920 4.5716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0117 -1.3028 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4890 4.1080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4890 4.1080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5651 3.7253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1200 3.0182 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4129 -0.5367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4890 -0.9194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5567 1.6401 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1420 -1.3022 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4129 3.7253 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4890 -0.9194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5027 2.0943 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.1200 0.1704 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.6988 0.3379 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4946 2.2894 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8544 1.7326 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5037 1.3187 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8580 3.0182 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5651 -0.5367 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5027 1.0943 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8352 1.5375 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9469 -0.3214 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4754 2.0943 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.8580 0.1704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1951 0.9808 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2555 1.9780 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.4835 0.8992 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1567 0.5906 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0266 -0.3852 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1759 0.7857 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0266 3.5737 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0096 -1.3682 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4754 1.0943 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 19 1 0 0 0 0 2 19 1 0 0 0 0 3 20 1 0 0 0 0 4 21 1 0 0 0 0 10 41 1 0 0 0 0 11 42 1 0 0 0 0 12 13 1 0 0 0 0 12 14 2 0 0 0 0 13 20 2 0 0 0 0 14 28 1 0 0 0 0 15 20 1 0 0 0 0 15 22 1 0 0 0 0 16 21 2 0 0 0 0 16 23 1 0 0 0 0 17 21 1 0 0 0 0 17 29 2 0 0 0 0 18 27 1 0 0 0 0 18 35 1 0 0 0 0 22 5 1 1 0 0 0 22 30 1 0 0 0 0 23 6 1 1 0 0 0 23 30 1 0 0 0 0 24 7 1 6 0 0 0 24 27 1 0 0 0 0 24 32 1 0 0 0 0 25 8 1 1 0 0 0 25 31 1 0 0 0 0 26 9 1 6 0 0 0 26 31 1 0 0 0 0 26 35 1 0 0 0 0 27 36 1 1 0 0 0 28 33 1 0 0 0 0 28 41 1 6 0 0 0 29 34 1 0 0 0 0 29 42 1 0 0 0 0 30 37 1 1 0 0 0 31 38 1 6 0 0 0 32 19 1 1 0 0 0 32 44 1 0 0 0 0 33 25 1 1 0 0 0 33 43 1 0 0 0 0 34 39 2 0 0 0 0 34 43 1 0 0 0 0 35 40 1 6 0 0 0 35 44 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	622.41
Volume:	662.733
LogP:	3.913
LogD:	3.289
LogS:	-4.703
# Rotatable Bonds:	7
TPSA:	134.91
# H-Bond Aceptor:	9
# H-Bond Donor:	4
# Rings:	2
# Heavy Atoms:	9

MedChem Properties

QED Drug-Likeness Score:	0.298
Synthetic Accessibility Score:	6.018
Fsp3:	0.743
Lipinski Rule-of-5:	Accepted
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:	-4.764
MDCK Permeability:	2.4827077140798792e-05
Pgp-inhibitor:	0.999
Pgp-substrate:	0.977
Human Intestinal Absorption (HIA):	0.546
20% Bioavailability (F20%):	0.288
30% Bioavailability (F30%):	0.699

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.013
Plasma Protein Binding (PPB):	92.81449890136719%
Volume Distribution (VD):	2.26
Pgp-substrate:	6.278058052062988%

ADMET: Metabolism

CYP1A2-inhibitor:	0.021
CYP1A2-substrate:	0.438
CYP2C19-inhibitor:	0.033
CYP2C19-substrate:	0.927
CYP2C9-inhibitor:	0.067
CYP2C9-substrate:	0.097
CYP2D6-inhibitor:	0.009
CYP2D6-substrate:	0.26
CYP3A4-inhibitor:	0.899
CYP3A4-substrate:	0.641

ADMET: Excretion

Clearance (CL):	7.18
Half-life (T1/2):	0.259

ADMET: Toxicity

hERG Blockers:	0.32
Human Hepatotoxicity (H-HT):	0.844
Drug-inuced Liver Injury (DILI):	0.645
AMES Toxicity:	0.026
Rat Oral Acute Toxicity:	0.039
Maximum Recommended Daily Dose:	0.026
Skin Sensitization:	0.841
Carcinogencity:	0.075
Eye Corrosion:	0.004
Eye Irritation:	0.013
Respiratory Toxicity:	0.743

Download Data

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

Natural Product: NPC288350

Natural Product ID:	NPC288350
*Common Name:**	Bafilomycin A1
IUPAC Name:	(3Z,5E,7R,8S,9S,11E,13E,15S,16R)-16-[(2S,3R,4S)-4-[(2R,4R,5S,6R)-2,4-dihydroxy-5-methyl-6-propan-2-yloxan-2-yl]-3-hydroxypentan-2-yl]-8-hydroxy-3,15-dimethoxy-5,7,9,11-tetramethyl-1-oxacyclohexadeca-3,5,11,13-tetraen-2-one
Synonyms:	Bafilomycin A1
Standard InCHIKey:	XDHNQDDQEHDUTM-JQWOJBOSSA-N
Standard InCHI:	InChI=1S/C35H58O9/c1-19(2)32-24(7)27(36)18-35(40,44-32)26(9)31(38)25(8)33-28(41-10)14-12-13-20(3)15-22(5)30(37)23(6)16-21(4)17-29(42-11)34(39)43-33/h12-14,16-17,19,22-28,30-33,36-38,40H,15,18H2,1-11H3/b14-12+,20-13+,21-16+,29-17-/t22-,23+,24-,25-,26-,27+,28-,30-,31+,32+,33+,35+/m0/s1
SMILES:	CO[C@H]1/C=C/C=C(C)/C[C@H](C)[C@H](O)[C@@H](/C=C(/C=C(/C(=O)O[C@@H]1[C@H]([C@H]([C@@H]([C@@]1(O)C[C@@H](O)[C@@H]([C@H](O1)C(C)C)C)C)O)C)OC)C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL290814
PubChem CID:	6436223
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000147] Macrolides and analogues

*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
NPO40774	Xestospongia ingens	Species	Petrosiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[33549907]
NPO9376	Tabernaemontana corymbosa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32356659]
NPO9376	Tabernaemontana corymbosa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30869890]
NPO40737	Characella sp.	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[29701963]
NPO9376	Tabernaemontana corymbosa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[29319316]
NPO9376	Tabernaemontana corymbosa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27077800]
NPO40536	Streptomyces albolongus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[26933756]
NPO9376	Tabernaemontana corymbosa	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26918761]
NPO9376	Tabernaemontana corymbosa	Species	Apocynaceae	Eukaryota	stem-bark	Pahang, Malaysia	2003-JUN	PMID[25919190]
NPO9376	Tabernaemontana corymbosa	Species	Apocynaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[24773071]

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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	1
IC50	11
Ki	1
Others	24

Activity Type	# Activity
Cell Line	15
Individual Protein	6
ORGANISM	1
Others	14
SINGLE PROTEIN	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	""	IC50	=	4.0	nM	PMID[451647]
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	13000.0	nM	PMID[451645]
NPT547	Cell Line	BGC-823	Homo sapiens	IC50	=	6470.0	nM	PMID[451643]
NPT492	Cell Line	Caco-2	Homo sapiens	IC50	=	5490.0	nM	PMID[451643]
NPT397	Cell Line	NCI-H460	Homo sapiens	IC50	=	12410.0	nM	PMID[451643]
NPT659	Cell Line	SMMC-7721	Homo sapiens	IC50	=	2030.0	nM	PMID[451643]
NPT35	Others	n.a.	""	permeability	=	27.4	%	PMID[451641]
NPT35	Others	n.a.	""	permeability	=	-1.5	%	PMID[451641]
NPT35	Others	n.a.	""	permeability	=	4.8	%	PMID[451641]
NPT35	Others	n.a.	""	permeability	=	90.5	%	PMID[451641]

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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 NPC288350 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	194
0.1-0.2	1160
0.2-0.3	3925
0.3-0.4	6938
0.4-0.5	16388
0.5-0.6	9661
0.6-0.7	3895
0.7-0.8	494
0.8-0.85	32
0.85-0.9	4
0.9-0.95	0
0.95-1	6

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC173329
0.89	High Similarity	NPC133625
0.8646	High Similarity	NPC120299
0.8557	High Similarity	NPC475653
0.8542	High Similarity	NPC255410

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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 NPC288350 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	174
0.1-0.2	1382
0.2-0.3	3502
0.3-0.4	2553
0.4-0.5	1160
0.5-0.6	306
0.6-0.7	65
0.7-0.8	6
0.8-0.85	2
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
0.8602	High Similarity	NPD7838	Discovery
0.8367	Intermediate Similarity	NPD8029	Clinical (unspecified phase)
0.7835	Intermediate Similarity	NPD6698	Approved
0.7835	Intermediate Similarity	NPD46	Approved
0.7404	Intermediate Similarity	NPD6648	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