NPASS Compound

Structure

CID198893 OpenBabel06191715582D 77 86 0 0 1 0 0 0 0 0999 V2000 -0.8660 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.5885 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -10.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -9.0000 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 0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.8564 -9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -9.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.9904 -8.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -8.5000 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 -0.0000 3.0000 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 6.0622 -7.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.3923 -7.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -7.0000 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 14.7224 -7.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.3301 -7.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 10.3923 -9.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -9.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.7942 -8.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 -5.5000 0.0000 C 0 0 2 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 14.7224 -8.5000 0.0000 C 0 0 1 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 -0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.9282 -7.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -5.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -8.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 11.2583 -7.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -7.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 12.9904 -7.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5981 -7.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0622 -8.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 -4.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 9.5263 -7.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -7.5000 0.0000 C 0 0 1 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 0.0000 -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 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 11.2583 -8.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -8.5000 0.0000 C 0 0 2 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 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7942 -7.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -6.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 15.5885 -9.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 O 0 0 0 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 -3.4641 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -6.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.1244 -9.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -9.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 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 13.8564 -7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5263 -8.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -8.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 -9.0000 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 5.1962 -9.0000 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 12.1244 -7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6603 -7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -7.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 21 1 0 0 0 0 8 10 2 0 0 0 0 8 30 1 0 0 0 0 9 12 1 0 0 0 0 9 29 1 0 0 0 0 10 36 1 0 0 0 0 11 13 1 0 0 0 0 11 35 1 0 0 0 0 12 39 1 0 0 0 0 13 40 1 0 0 0 0 14 21 2 0 0 0 0 14 28 1 0 0 0 0 15 21 1 0 0 0 0 15 31 2 0 0 0 0 16 28 1 0 0 0 0 16 32 1 0 0 0 0 17 33 1 0 0 0 0 17 41 1 0 0 0 0 18 34 1 0 0 0 0 18 42 1 0 0 0 0 19 37 1 0 0 0 0 19 43 1 0 0 0 0 20 38 1 0 0 0 0 20 44 1 0 0 0 0 22 2 1 1 0 0 0 22 29 1 0 0 0 0 22 66 1 0 0 0 0 23 3 1 1 0 0 0 23 35 1 0 0 0 0 23 67 1 0 0 0 0 24 4 1 1 0 0 0 24 50 1 0 0 0 0 24 68 1 0 0 0 0 25 5 1 1 0 0 0 25 51 1 0 0 0 0 25 69 1 0 0 0 0 26 6 1 1 0 0 0 26 54 1 0 0 0 0 26 70 1 0 0 0 0 27 7 1 1 0 0 0 27 55 1 0 0 0 0 27 71 1 0 0 0 0 28 45 2 0 0 0 0 29 56 1 1 0 0 0 30 46 2 0 0 0 0 30 57 1 0 0 0 0 31 45 1 0 0 0 0 31 58 1 0 0 0 0 32 47 1 0 0 0 0 32 59 1 6 0 0 0 33 54 1 0 0 0 0 33 60 1 1 0 0 0 34 55 1 0 0 0 0 34 61 1 1 0 0 0 35 72 1 1 0 0 0 36 48 2 0 0 0 0 36 73 1 0 0 0 0 37 50 1 0 0 0 0 37 74 1 1 0 0 0 38 51 1 0 0 0 0 38 75 1 1 0 0 0 39 66 1 0 0 0 0 39 74 1 6 0 0 0 40 67 1 0 0 0 0 40 75 1 6 0 0 0 41 70 1 0 0 0 0 41 72 1 1 0 0 0 42 71 1 0 0 0 0 42 73 1 1 0 0 0 43 68 1 0 0 0 0 43 76 1 1 0 0 0 44 69 1 0 0 0 0 44 77 1 1 0 0 0 45 49 1 0 0 0 0 46 48 1 0 0 0 0 46 53 1 0 0 0 0 47 49 2 0 0 0 0 47 52 1 0 0 0 0 48 52 1 0 0 0 0 49 53 1 0 0 0 0 50 62 1 6 0 0 0 51 63 1 6 0 0 0 52 64 2 0 0 0 0 53 65 2 0 0 0 0 54 76 1 6 0 0 0 55 77 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1086.47
Volume:	1043.928
LogP:	6.276
LogD:	3.033
LogS:	-5.915
# Rotatable Bonds:	12
TPSA:	313.06
# H-Bond Aceptor:	22
# H-Bond Donor:	10
# Rings:	10
# Heavy Atoms:	22

MedChem Properties

QED Drug-Likeness Score:	0.052
Synthetic Accessibility Score:	6.811
Fsp3:	0.673
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.223
MDCK Permeability:	0.00021440477576106787
Pgp-inhibitor:	0.0
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.023
20% Bioavailability (F20%):	0.0
30% Bioavailability (F30%):	0.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.096
Plasma Protein Binding (PPB):	93.71587371826172%
Volume Distribution (VD):	-0.341
Pgp-substrate:	11.415776252746582%

ADMET: Metabolism

CYP1A2-inhibitor:	0.002
CYP1A2-substrate:	0.985
CYP2C19-inhibitor:	0.029
CYP2C19-substrate:	0.503
CYP2C9-inhibitor:	0.043
CYP2C9-substrate:	0.141
CYP2D6-inhibitor:	0.004
CYP2D6-substrate:	0.115
CYP3A4-inhibitor:	0.029
CYP3A4-substrate:	0.757

ADMET: Excretion

Clearance (CL):	1.345
Half-life (T1/2):	0.162

ADMET: Toxicity

hERG Blockers:	0.318
Human Hepatotoxicity (H-HT):	0.215
Drug-inuced Liver Injury (DILI):	0.99
AMES Toxicity:	0.573
Rat Oral Acute Toxicity:	0.142
Maximum Recommended Daily Dose:	0.984
Skin Sensitization:	0.966
Carcinogencity:	0.894
Eye Corrosion:	0.003
Eye Irritation:	0.018
Respiratory Toxicity:	0.808

Download Data

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

Natural Product: NPC198893

Natural Product ID:	NPC198893
*Common Name:**	Landomycin A
IUPAC Name:	(6R)-1,6,11-trihydroxy-8-[(2S,4R,5S,6R)-4-hydroxy-5-[(2S,4R,5R,6R)-5-hydroxy-4-[(2S,5S,6S)-5-[(2S,4R,5S,6R)-4-hydroxy-5-[(2S,4R,5R,6R)-5-hydroxy-4-[(2S,5S,6S)-5-hydroxy-6-methyloxan-2-yl]oxy-6-methyloxan-2-yl]oxy-6-methyloxan-2-yl]oxy-6-methyloxan-2-yl]oxy-6-methyloxan-2-yl]oxy-6-methyloxan-2-yl]oxy-3-methyl-5,6-dihydrobenzo[a]anthracene-7,12-dione
Synonyms:	Landomycin A
Standard InCHIKey:	YMSZNAXJMXNNPT-OPAYXXSESA-N
Standard InCHI:	InChI=1S/C55H74O22/c1-21-14-28-16-32(59)47-49(45(28)31(58)15-21)53(65)46-30(57)8-10-36(48(46)52(47)64)73-42-18-34(61)55(27(7)71-42)77-44-20-38(51(63)25(5)69-44)75-40-13-11-35(23(3)67-40)72-41-17-33(60)54(26(6)70-41)76-43-19-37(50(62)24(4)68-43)74-39-12-9-29(56)22(2)66-39/h8,10,14-15,22-27,29,32-35,37-44,50-51,54-63H,9,11-13,16-20H2,1-7H3/t22-,23-,24+,25+,26+,27+,29-,32+,33+,34+,35-,37+,38+,39-,40-,41-,42-,43-,44-,50+,51+,54+,55+/m0/s1
SMILES:	Cc1cc2C[C@H](C3=C(c2c(c1)O)C(=O)c1c(ccc(c1C3=O)O[C@H]1C[C@H]([C@@H]([C@@H](C)O1)O[C@H]1C[C@H]([C@@H]([C@@H](C)O1)O)O[C@H]1CC[C@@H]([C@H](C)O1)O[C@H]1C[C@H]([C@@H]([C@@H](C)O1)O[C@H]1C[C@H]([C@@H]([C@@H](C)O1)O)O[C@H]1CC[C@@H]([C@H](C)O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1668770
PubChem CID:	9988748
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000018] Anthracenes [CHEMONTID:0000151] Anthraquinones

*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
GI50	2
IC50	2
Others	9

Activity Type	# Activity
Cell Line	3
NON-MOLECULAR	1
Organism	9

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT306	Cell Line	PC-3	Homo sapiens	GI50	=	550.5	nM	PMID[512843]
NPT397	Cell Line	NCI-H460	Homo sapiens	GI50	=	4109.0	nM	PMID[512843]
NPT83	Cell Line	MCF7	Homo sapiens	IC50	=	2500.0	nM	PMID[512842]
NPT20529	NON-MOLECULAR	NON-PROTEIN TARGET	n.a.	IC50	=	1400.0	nM	PMID[512842]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	10000.0	c.p.m./Abs	PMID[512841]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	45000.0	c.p.m./Abs	PMID[512841]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	65000.0	c.p.m./Abs	PMID[512841]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	5000.0	c.p.m./Abs	PMID[512841]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	30000.0	c.p.m./Abs	PMID[512841]
NPT32	Organism	Mus musculus	Mus musculus	Inhibition	=	60000.0	c.p.m./Abs	PMID[512841]

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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 NPC198893 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	445
0.1-0.2	1644
0.2-0.3	3484
0.3-0.4	8406
0.4-0.5	9003
0.5-0.6	6754
0.6-0.7	8109
0.7-0.8	4480
0.8-0.85	270
0.85-0.9	78
0.9-0.95	14
0.95-1	10

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC232818
1.0	High Similarity	NPC314489
0.9817	High Similarity	NPC307754
0.9817	High Similarity	NPC223735
0.9816	High Similarity	NPC315619

Showing 1 to 5 of 200 entries

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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 NPC198893 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	387
0.1-0.2	941
0.2-0.3	1802
0.3-0.4	2794
0.4-0.5	1945
0.5-0.6	895
0.6-0.7	298
0.7-0.8	79
0.8-0.85	7
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
0.8953	High Similarity	NPD8312	Approved
0.8953	High Similarity	NPD8313	Approved
0.8603	High Similarity	NPD7879	Clinical (unspecified phase)
0.8343	Intermediate Similarity	NPD7804	Clinical (unspecified phase)
0.8295	Intermediate Similarity	NPD7074	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