NPASS Compound

Structure

CID197357 OpenBabel06191715582D 67 75 0 0 1 0 0 0 0 0999 V2000 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -5.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -6.0000 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 1.7321 0.0000 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 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -2.0000 0.0000 C 0 0 0 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 -2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 5.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -3.5000 0.0000 C 0 0 0 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 8.6603 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 12.9904 4.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7942 -4.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 11.2583 2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 -5.0000 0.0000 C 0 0 2 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 -0.5000 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 -1.7321 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 6.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 9.5263 2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -3.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 9.5263 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7942 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 10.3923 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -3.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 11.2583 4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0622 -4.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 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 -0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 5.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7942 -3.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 3.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -4.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -3.0000 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 -0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 4.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -5.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 20 1 0 0 0 0 7 8 2 0 0 0 0 7 9 1 0 0 0 0 8 27 1 0 0 0 0 9 34 2 0 0 0 0 10 11 2 0 0 0 0 10 26 1 0 0 0 0 11 28 1 0 0 0 0 12 13 1 0 0 0 0 12 33 1 0 0 0 0 13 36 1 0 0 0 0 14 20 2 0 0 0 0 14 26 1 0 0 0 0 15 20 1 0 0 0 0 15 29 2 0 0 0 0 16 30 1 0 0 0 0 16 39 1 0 0 0 0 17 31 1 0 0 0 0 17 37 1 0 0 0 0 18 32 1 0 0 0 0 18 38 1 0 0 0 0 19 35 1 0 0 0 0 19 40 1 0 0 0 0 21 2 1 1 0 0 0 21 33 1 0 0 0 0 21 58 1 0 0 0 0 22 3 1 1 0 0 0 22 44 1 0 0 0 0 22 59 1 0 0 0 0 23 4 1 1 0 0 0 23 45 1 0 0 0 0 23 60 1 0 0 0 0 24 5 1 1 0 0 0 24 48 1 0 0 0 0 24 61 1 0 0 0 0 25 6 1 1 0 0 0 25 49 1 0 0 0 0 25 62 1 0 0 0 0 26 41 2 0 0 0 0 27 42 2 0 0 0 0 27 47 1 0 0 0 0 28 43 2 0 0 0 0 28 46 1 0 0 0 0 29 41 1 0 0 0 0 29 50 1 0 0 0 0 30 44 1 0 0 0 0 30 51 1 1 0 0 0 31 48 1 0 0 0 0 31 52 1 1 0 0 0 32 49 1 0 0 0 0 32 53 1 1 0 0 0 33 63 1 1 0 0 0 34 42 1 0 0 0 0 34 64 1 0 0 0 0 35 45 1 0 0 0 0 35 65 1 1 0 0 0 36 58 1 0 0 0 0 36 65 1 6 0 0 0 37 61 1 0 0 0 0 37 63 1 1 0 0 0 38 62 1 0 0 0 0 38 64 1 1 0 0 0 39 59 1 0 0 0 0 39 66 1 1 0 0 0 40 60 1 0 0 0 0 40 67 1 1 0 0 0 41 43 1 0 0 0 0 42 46 1 0 0 0 0 43 47 1 0 0 0 0 44 54 1 6 0 0 0 45 55 1 6 0 0 0 46 56 2 0 0 0 0 47 57 2 0 0 0 0 48 66 1 6 0 0 0 49 67 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	938.39
Volume:	910.911
LogP:	5.031
LogD:	3.031
LogS:	-6.79
# Rotatable Bonds:	10
TPSA:	247.82
# H-Bond Aceptor:	18
# H-Bond Donor:	6
# Rings:	9
# Heavy Atoms:	18

MedChem Properties

QED Drug-Likeness Score:	0.133
Synthetic Accessibility Score:	6.259
Fsp3:	0.633
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	2

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.681
MDCK Permeability:	0.00014343087968882173
Pgp-inhibitor:	0.0
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.008
20% Bioavailability (F20%):	0.0
30% Bioavailability (F30%):	0.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.015
Plasma Protein Binding (PPB):	92.52967834472656%
Volume Distribution (VD):	0.32
Pgp-substrate:	5.944314002990723%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.966
CYP2C19-inhibitor:	0.073
CYP2C19-substrate:	0.478
CYP2C9-inhibitor:	0.171
CYP2C9-substrate:	0.022
CYP2D6-inhibitor:	0.014
CYP2D6-substrate:	0.122
CYP3A4-inhibitor:	0.152
CYP3A4-substrate:	0.914

ADMET: Excretion

Clearance (CL):	2.04
Half-life (T1/2):	0.021

ADMET: Toxicity

hERG Blockers:	0.768
Human Hepatotoxicity (H-HT):	0.232
Drug-inuced Liver Injury (DILI):	0.986
AMES Toxicity:	0.798
Rat Oral Acute Toxicity:	0.725
Maximum Recommended Daily Dose:	0.989
Skin Sensitization:	0.888
Carcinogencity:	0.898
Eye Corrosion:	0.003
Eye Irritation:	0.037
Respiratory Toxicity:	0.294

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

Natural Product: NPC197357

Natural Product ID:	NPC197357
*Common Name:**	Landomycin M
IUPAC Name:	8-[(2S,4R,5S,6R)-5-[(2S,4R,5R,6R)-4-[(2S,5S,6S)-5-[(2S,4R,5S,6R)-5-[(2S,4R,5S,6R)-4,5-dihydroxy-6-methyloxan-2-yl]oxy-4-hydroxy-6-methyloxan-2-yl]oxy-6-methyloxan-2-yl]oxy-5-hydroxy-6-methyloxan-2-yl]oxy-4-hydroxy-6-methyloxan-2-yl]oxy-1-hydroxy-3-methylbenzo[a]anthracene-7,12-dione
Synonyms:	Landomycin M
Standard InCHIKey:	CIMVKHLLOLGAFV-UYCWPDQGSA-N
Standard InCHI:	InChI=1S/C49H62O18/c1-20-14-26-10-11-28-43(41(26)29(50)15-20)47(57)27-8-7-9-34(42(27)46(28)56)64-38-18-32(53)49(25(6)62-38)67-40-19-35(45(55)23(4)60-40)65-36-13-12-33(21(2)58-36)63-37-17-31(52)48(24(5)61-37)66-39-16-30(51)44(54)22(3)59-39/h7-11,14-15,21-25,30-33,35-40,44-45,48-55H,12-13,16-19H2,1-6H3/t21-,22+,23+,24+,25+,30+,31+,32+,33-,35+,36-,37-,38-,39-,40-,44+,45+,48+,49+/m0/s1
SMILES:	Cc1cc(O)c2c(c1)ccc1c2C(=O)c2c(C1=O)c(ccc2)O[C@H]1C[C@@H](O)[C@@H]([C@H](O1)C)O[C@@H]1O[C@H](C)[C@H]([C@@H](C1)O[C@H]1CC[C@@H]([C@@H](O1)C)O[C@H]1C[C@@H](O)[C@@H]([C@H](O1)C)O[C@H]1C[C@@H](O)[C@@H]([C@H](O1)C)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1668762
PubChem CID:	53324863
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003415] Angucyclines

*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
NPO19685	Streptomyces cyanogenus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21188999]
NPO19685	Streptomyces cyanogenus	Species	Streptomycetaceae	Bacteria	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
IC50	2

Activity Type	# Activity
Cell Line	1
NON-MOLECULAR	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	7100.0	nM	PMID[476897]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	1900.0	nM	PMID[476897]

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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 NPC197357 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	453
0.1-0.2	1677
0.2-0.3	3459
0.3-0.4	8331
0.4-0.5	9158
0.5-0.6	6631
0.6-0.7	6898
0.7-0.8	5364
0.8-0.85	578
0.85-0.9	113
0.9-0.95	26
0.95-1	9

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC85316
0.9881	High Similarity	NPC292706
0.9881	High Similarity	NPC224557
0.9819	High Similarity	NPC289876
0.9702	High Similarity	NPC58538

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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 NPC197357 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	404
0.1-0.2	935
0.2-0.3	1803
0.3-0.4	2751
0.4-0.5	2002
0.5-0.6	858
0.6-0.7	290
0.7-0.8	92
0.8-0.85	13
0.85-0.9	0
0.9-0.95	2
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.924	High Similarity	NPD8312	Approved
0.924	High Similarity	NPD8313	Approved
0.8771	High Similarity	NPD7879	Clinical (unspecified phase)
0.8409	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.8382	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