NPASS Compound

Structure

CID197736 OpenBabel06191715582D 71 75 0 0 1 0 0 0 0 0999 V2000 -6.5705 6.7003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5618 -7.4059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6157 4.0516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0376 -0.2863 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5705 6.7003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0705 5.8343 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9925 -1.2029 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9925 -2.9350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0705 7.5663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6831 -5.2846 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0705 2.3702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7865 -8.6306 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0705 5.8343 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2689 -6.6988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3300 1.5481 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7520 2.2172 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0086 0.6012 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4305 3.1641 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2646 2.5460 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6866 1.2193 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7712 3.9160 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3492 -0.1506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0705 2.3702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8888 -7.8542 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5705 4.9682 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7853 -4.5081 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8223 3.4429 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.2443 0.3225 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0705 5.8343 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5705 4.9682 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9925 -1.2029 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.9925 -2.9350 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5705 6.7003 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.7172 -5.0257 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.0705 2.3702 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8206 -8.3718 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0705 5.8343 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.0101 -5.7328 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.5705 1.5041 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1476 -8.8201 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0705 5.8343 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5705 4.9682 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0442 -5.4740 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8743 4.3582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5477 -0.5929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5705 3.2362 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5959 -7.1471 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5705 4.9682 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4925 -2.0689 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5705 1.5041 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.1135 -9.0789 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0705 4.1022 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4925 -0.3369 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4925 -3.8010 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.0705 0.6381 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4405 -9.5272 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1331 5.3242 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2888 -1.5589 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0705 4.1022 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4925 -2.0689 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0705 0.6381 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3723 -10.0448 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5010 -3.6705 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5705 6.7003 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5705 3.2362 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5618 -7.4059 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0705 4.1022 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.3371 -6.1811 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8765 4.4236 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5455 -0.6583 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4584 -4.0598 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 13 1 0 0 0 0 2 14 1 0 0 0 0 15 17 1 0 0 0 0 15 19 2 0 0 0 0 16 18 1 0 0 0 0 16 20 2 0 0 0 0 17 22 2 0 0 0 0 18 21 2 0 0 0 0 19 27 1 0 0 0 0 20 28 1 0 0 0 0 21 44 1 0 0 0 0 22 45 1 0 0 0 0 23 39 1 0 0 0 0 23 46 1 0 0 0 0 24 40 1 0 0 0 0 24 47 1 0 0 0 0 25 41 2 0 0 0 0 25 42 1 0 0 0 0 26 43 1 0 0 0 0 26 54 1 0 0 0 0 27 3 1 6 0 0 0 27 52 1 0 0 0 0 28 4 1 6 0 0 0 28 53 1 0 0 0 0 29 5 1 1 0 0 0 29 41 1 0 0 0 0 29 48 1 0 0 0 0 30 6 1 6 0 0 0 30 48 1 0 0 0 0 31 7 1 1 0 0 0 31 49 1 0 0 0 0 32 8 1 6 0 0 0 32 49 1 0 0 0 0 32 54 1 0 0 0 0 33 9 1 1 0 0 0 33 37 1 0 0 0 0 33 64 1 0 0 0 0 34 10 1 6 0 0 0 34 38 1 0 0 0 0 34 71 1 0 0 0 0 35 11 1 1 0 0 0 35 50 1 0 0 0 0 35 65 1 0 0 0 0 36 12 1 1 0 0 0 36 51 1 0 0 0 0 36 66 1 0 0 0 0 37 13 1 6 0 0 0 37 42 1 0 0 0 0 38 14 1 1 0 0 0 38 43 1 0 0 0 0 39 50 1 0 0 0 0 39 55 1 1 0 0 0 40 51 1 0 0 0 0 40 56 1 1 0 0 0 41 64 1 0 0 0 0 42 67 1 1 0 0 0 43 68 1 6 0 0 0 44 57 2 0 0 0 0 44 69 1 0 0 0 0 45 58 2 0 0 0 0 45 70 1 0 0 0 0 46 65 1 0 0 0 0 46 67 1 6 0 0 0 47 66 1 0 0 0 0 47 68 1 6 0 0 0 48 59 1 1 0 0 0 49 60 1 6 0 0 0 50 61 1 1 0 0 0 51 62 1 1 0 0 0 52 30 1 1 0 0 0 52 69 1 0 0 0 0 53 31 1 1 0 0 0 53 70 1 0 0 0 0 54 63 1 1 0 0 0 54 71 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1006.59
Volume:	1030.736
LogP:	6.096
LogD:	4.847
LogS:	-4.838
# Rotatable Bonds:	14
TPSA:	249.59
# H-Bond Aceptor:	17
# H-Bond Donor:	7
# Rings:	5
# Heavy Atoms:	17

MedChem Properties

QED Drug-Likeness Score:	0.114
Synthetic Accessibility Score:	7.585
Fsp3:	0.778
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.37
MDCK Permeability:	0.00039489578921347857
Pgp-inhibitor:	1.0
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.835
20% Bioavailability (F20%):	0.189
30% Bioavailability (F30%):	0.696

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.001
Plasma Protein Binding (PPB):	88.10501098632812%
Volume Distribution (VD):	0.89
Pgp-substrate:	5.921917915344238%

ADMET: Metabolism

CYP1A2-inhibitor:	0.003
CYP1A2-substrate:	0.067
CYP2C19-inhibitor:	0.016
CYP2C19-substrate:	0.914
CYP2C9-inhibitor:	0.013
CYP2C9-substrate:	0.009
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.033
CYP3A4-inhibitor:	0.614
CYP3A4-substrate:	0.913

ADMET: Excretion

Clearance (CL):	5.369
Half-life (T1/2):	0.054

ADMET: Toxicity

hERG Blockers:	0.676
Human Hepatotoxicity (H-HT):	0.513
Drug-inuced Liver Injury (DILI):	0.033
AMES Toxicity:	0.054
Rat Oral Acute Toxicity:	0.134
Maximum Recommended Daily Dose:	0.991
Skin Sensitization:	0.948
Carcinogencity:	0.115
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.985

Download Data

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

Natural Product: NPC197736

Natural Product ID:	NPC197736
*Common Name:**	11',12'-Dehydroelaiophylin
IUPAC Name:	(3E,5E,7S,8S,11E,13E,15S,16S)-8-[(2S,3R,4S)-4-[(2R,4R,5R,6R)-4-[(2R,4S,5S,6S)-4,5-dihydroxy-6-methyloxan-2-yl]oxy-5-ethyl-2-hydroxy-6-methyloxan-2-yl]-3-hydroxypentan-2-yl]-16-[(2S,3R,4S)-4-[(2R,3R,4S)-4-[(2R,4S,5S,6S)-4,5-dihydroxy-6-methyloxan-2-yl]oxy-3-ethyl-2-methyl-3,4-dihydro-2H-pyran-6-yl]-3-hydroxypentan-2-yl]-7,15-dimethyl-1,9-dioxacyclohexadeca-3,5,11,13-tetraene-2,10-dione
Synonyms:
Standard InCHIKey:	OSJLHWZHXOEYPJ-JRNNISHJSA-N
Standard InCHI:	InChI=1S/C54H86O17/c1-13-37-33(9)64-41(25-42(37)67-46-23-39(55)50(61)35(11)65-46)29(5)48(59)30(6)52-27(3)19-15-17-22-45(58)70-53(28(4)20-16-18-21-44(57)69-52)31(7)49(60)32(8)54(63)26-43(38(14-2)34(10)71-54)68-47-24-40(56)51(62)36(12)66-47/h15-22,25,27-40,42-43,46-53,55-56,59-63H,13-14,23-24,26H2,1-12H3/b19-15+,20-16+,21-18+,22-17+/t27-,28-,29+,30-,31-,32-,33+,34+,35-,36-,37+,38+,39-,40-,42+,43+,46-,47-,48-,49+,50+,51+,52-,53-,54+/m0/s1
SMILES:	CC[C@@H]1[C@@H](C)OC(=C[C@H]1O[C@H]1C[C@@H]([C@@H]([C@H](C)O1)O)O)[C@@H](C)[C@@H]([C@H](C)[C@@H]1[C@@H](C)/C=C/C=C/C(=O)O[C@@H]([C@@H](C)/C=C/C=C/C(=O)O1)[C@@H](C)[C@H]([C@H](C)[C@]1(C[C@H]([C@H](CC)[C@@H](C)O1)O[C@H]1C[C@@H]([C@@H]([C@H](C)O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL3086647
PubChem CID:	72945493
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
NPO32916	Streptomyces sp. 7-145	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[24164206]

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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
MIC	22

Activity Type	# Activity
NON-MOLECULAR	1
Organism	21

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT3495	Organism	Morganella morganii	Morganella morganii	MIC	>	64.0	ug.mL-1	PMID[556245]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	64.0	ug.mL-1	PMID[556245]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	MIC	>	64.0	ug.mL-1	PMID[556245]
NPT173	Organism	Klebsiella pneumoniae	Klebsiella pneumoniae	MIC	>	64.0	ug.mL-1	PMID[556245]
NPT19	Organism	Escherichia coli	Escherichia coli	MIC	>	64.0	ug.mL-1	PMID[556245]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	>	64.0	ug.mL-1	PMID[556245]
NPT17	Organism	Staphylococcus epidermidis	Staphylococcus epidermidis	MIC	>	64.0	ug.mL-1	PMID[556245]
NPT1277	Organism	Staphylococcus epidermidis ATCC 12228	Staphylococcus epidermidis ATCC 12228	MIC	>	64.0	ug.mL-1	PMID[556245]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	>	64.0	ug.mL-1	PMID[556245]
NPT1531	Organism	Enterococcus faecium	Enterococcus faecium	MIC	=	4.0	ug.mL-1	PMID[556245]

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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 NPC197736 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	217
0.1-0.2	1303
0.2-0.3	4232
0.3-0.4	8707
0.4-0.5	14316
0.5-0.6	9635
0.6-0.7	3553
0.7-0.8	682
0.8-0.85	36
0.85-0.9	4
0.9-0.95	11
0.95-1	1

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Similarity Score	Similarity Level	Natural Product ID
0.9583	High Similarity	NPC475157
0.9583	High Similarity	NPC471637
0.9583	High Similarity	NPC154132
0.9583	High Similarity	NPC2313
0.9583	High Similarity	NPC475655

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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 NPC197736 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	191
0.1-0.2	1412
0.2-0.3	3706
0.3-0.4	2530
0.4-0.5	986
0.5-0.6	265
0.6-0.7	46
0.7-0.8	13
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
0.8235	Intermediate Similarity	NPD8029	Clinical (unspecified phase)
0.79	Intermediate Similarity	NPD7838	Discovery
0.7759	Intermediate Similarity	NPD7503	Approved
0.7607	Intermediate Similarity	NPD8513	Phase 3
0.7589	Intermediate Similarity	NPD8413	Clinical (unspecified phase)

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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