NPASS Compound

Structure

NPC469673 OpenBabel07101719192D 54 62 0 0 1 0 0 0 0 0999 V2000 -0.5401 -3.4761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4141 1.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3626 -2.5191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5539 1.0879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2622 2.7439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3521 -0.6623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1307 -0.2398 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7517 -2.3379 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1069 -2.0196 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2816 -1.1518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8002 -2.3693 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5989 -0.5502 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1248 0.3310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0200 -2.1672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3124 -2.5236 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5660 1.7646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3077 -1.2542 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5887 0.2201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7060 -0.3596 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9914 -0.0354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7133 -1.9907 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0847 -2.1048 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4567 -1.3337 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4243 -1.1338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7842 0.0879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2821 1.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3338 -1.1518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1302 -0.1940 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2821 0.2957 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.6016 -1.4648 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.1302 1.7646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0996 -1.0875 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9783 1.2750 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1634 -2.5566 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5660 2.7439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2144 0.3239 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7071 -1.6024 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9783 0.2957 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.3079 -1.7869 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2418 -0.3040 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4035 -1.1469 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3307 0.9004 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5137 -3.4214 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1302 2.7439 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8264 1.7646 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2574 -3.5314 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2821 3.2336 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1286 1.2412 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1191 -1.2383 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4141 3.2336 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3395 -1.6032 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3500 0.2853 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6242 -2.4334 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 15 1 0 0 0 0 2 16 1 0 0 0 0 5 50 1 0 0 0 0 6 7 1 0 0 0 0 6 24 1 0 0 0 0 7 25 1 0 0 0 0 8 9 1 0 0 0 0 8 15 2 0 0 0 0 9 51 1 0 0 0 0 10 19 1 0 0 0 0 11 21 1 0 0 0 0 11 22 1 0 0 0 0 12 20 1 0 0 0 0 12 23 1 0 0 0 0 13 18 1 0 0 0 0 13 52 1 0 0 0 0 14 53 1 0 0 0 0 15 34 1 0 0 0 0 16 26 2 0 0 0 0 16 35 1 0 0 0 0 17 10 1 1 0 0 0 17 19 1 0 0 0 0 17 27 1 0 0 0 0 18 20 2 0 0 0 0 18 36 1 0 0 0 0 19 38 1 1 0 0 0 20 40 1 0 0 0 0 21 22 1 0 0 0 0 21 37 1 1 0 0 0 22 39 1 1 0 0 0 23 37 1 6 0 0 0 23 39 1 0 0 0 0 24 41 2 0 0 0 0 24 51 1 0 0 0 0 25 42 2 0 0 0 0 25 52 1 0 0 0 0 26 29 1 0 0 0 0 26 31 1 0 0 0 0 27 28 2 0 0 0 0 27 30 1 0 0 0 0 28 29 1 0 0 0 0 28 38 1 0 0 0 0 29 40 1 6 0 0 0 30 32 1 0 0 0 0 30 43 1 1 0 0 0 31 33 1 0 0 0 0 31 44 2 0 0 0 0 32 37 1 6 0 0 0 32 40 1 0 0 0 0 33 38 1 1 0 0 0 33 45 1 0 0 0 0 34 46 2 0 0 0 0 34 53 1 0 0 0 0 35 47 2 0 0 0 0 35 50 1 0 0 0 0 36 48 2 0 0 0 0 36 54 1 0 0 0 0 37 3 1 1 0 0 0 38 4 1 1 0 0 0 39 14 1 6 0 0 0 39 49 1 0 0 0 0 40 54 1 1 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	748.27
Volume:	720.086
LogP:	2.823
LogD:	2.649
LogS:	-4.509
# Rotatable Bonds:	2
TPSA:	206.1
# H-Bond Aceptor:	14
# H-Bond Donor:	2
# Rings:	9
# Heavy Atoms:	14

MedChem Properties

QED Drug-Likeness Score:	0.169
Synthetic Accessibility Score:	5.128
Fsp3:	0.675
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.211
MDCK Permeability:	0.0001234072115039453
Pgp-inhibitor:	1.0
Pgp-substrate:	0.687
Human Intestinal Absorption (HIA):	0.247
20% Bioavailability (F20%):	0.993
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.092
Plasma Protein Binding (PPB):	63.52051544189453%
Volume Distribution (VD):	0.401
Pgp-substrate:	17.757343292236328%

ADMET: Metabolism

CYP1A2-inhibitor:	0.015
CYP1A2-substrate:	0.764
CYP2C19-inhibitor:	0.419
CYP2C19-substrate:	0.221
CYP2C9-inhibitor:	0.753
CYP2C9-substrate:	0.008
CYP2D6-inhibitor:	0.015
CYP2D6-substrate:	0.021
CYP3A4-inhibitor:	0.866
CYP3A4-substrate:	0.576

ADMET: Excretion

Clearance (CL):	8.004
Half-life (T1/2):	0.274

ADMET: Toxicity

hERG Blockers:	0.377
Human Hepatotoxicity (H-HT):	0.192
Drug-inuced Liver Injury (DILI):	0.437
AMES Toxicity:	0.021
Rat Oral Acute Toxicity:	0.074
Maximum Recommended Daily Dose:	0.963
Skin Sensitization:	0.351
Carcinogencity:	0.048
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.698

Download Data

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

Natural Product: NPC469673

Natural Product ID:	NPC469673
*Common Name:**	Chloramultiol A
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	JTARRSXSYCCLKA-ZSNYSFAYSA-N
Standard InCHI:	InChI=1S/C40H44O14/c1-15-8-9-51-24(41)6-7-25(42)52-13-18-20-12-23-37(3,21-11-22(21)39(23,49)14-53-34(15)46)32-30(43)27-17-10-19(17)38(4)28(27)29(40(20,32)54-36(18)48)26(31(44)33(38)45)16(2)35(47)50-5/h8,17,19,21-23,29-30,32-33,43,45,49H,6-7,9-14H2,1-5H3/b15-8+,26-16-/t17-,19+,21+,22-,23+,29-,30-,32-,33-,37-,38-,39-,40+/m0/s1
SMILES:	COC(=O)/C(=C/1C(=O)[C@H](O)[C@@]2(C3=C([C@@H]([C@@H]4[C@@]5([C@@H]13)OC(=O)C1=C5C[C@@H]3[C@]4(C)[C@@H]4C[C@@H]4[C@@]3(O)COC(=O)/C(=C/COC(=O)CCC(=O)OC1)/C)O)[C@@H]1[C@H]2C1)C)/C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1097986
PubChem CID:	46834846
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

*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
NPO8670	Chloranthus multistachys	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20392109]
NPO8670	Chloranthus multistachys	Species	Chloranthaceae	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
IC50	5

Activity Type	# Activity
Cell Line	5

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT81	Cell Line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[564997]
NPT116	Cell Line	HL-60	Homo sapiens	IC50	>	10000.0	nM	PMID[564997]
NPT461	Cell Line	PANC-1	Homo sapiens	IC50	>	10000.0	nM	PMID[564997]
NPT659	Cell Line	SMMC-7721	Homo sapiens	IC50	>	10000.0	nM	PMID[564997]
NPT134	Cell Line	SK-BR-3	Homo sapiens	IC50	>	10000.0	nM	PMID[564997]

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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 NPC469673 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	309
0.1-0.2	1654
0.2-0.3	4840
0.3-0.4	8294
0.4-0.5	12469
0.5-0.6	7314
0.6-0.7	5773
0.7-0.8	1859
0.8-0.85	129
0.85-0.9	28
0.9-0.95	5
0.95-1	23

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Similarity Score	Similarity Level	Natural Product ID
0.9918	High Similarity	NPC476823
0.9917	High Similarity	NPC34963
0.9836	High Similarity	NPC58029
0.9835	High Similarity	NPC196921
0.9835	High Similarity	NPC220757

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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 NPC469673 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	258
0.1-0.2	1868
0.2-0.3	3875
0.3-0.4	2062
0.4-0.5	626
0.5-0.6	228
0.6-0.7	155
0.7-0.8	77
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
0.824	Intermediate Similarity	NPD7115	Discovery
0.8047	Intermediate Similarity	NPD6319	Approved
0.792	Intermediate Similarity	NPD8297	Approved
0.784	Intermediate Similarity	NPD6649	Approved
0.784	Intermediate Similarity	NPD6650	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