NPASS Compound

Structure

NPC29679 OpenBabel06302215102D 70 71 0 0 1 0 0 0 0 0999 V2000 -2.1032 -1.2927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1659 -0.9441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9991 0.0419 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9564 0.3309 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8118 0.8489 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.5115 1.5634 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.3080 0.9588 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0115 2.4294 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2804 3.3926 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.3013 4.3924 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2959 4.4969 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8836 3.6879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8782 3.7924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4769 2.7743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0730 5.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6097 6.2522 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.9406 6.9953 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1076 7.5487 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1633 7.8776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1668 7.9612 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.8192 7.7945 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1083 8.7518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4237 9.4808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5499 9.2524 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2344 9.9814 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.2080 9.7530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8925 10.4820 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.4970 8.7957 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.7328 7.3877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5165 6.7666 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.1211 5.9701 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.9871 6.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8531 5.9701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7191 6.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5852 5.9701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.4512 6.4701 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 7.4512 7.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3172 5.9701 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 8.3172 4.9701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1832 4.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1832 3.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0493 2.9701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.9153 3.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.9153 4.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.0493 4.9701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1832 6.4701 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.1832 7.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7191 7.4701 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5086 5.0482 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.4717 5.3171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6547 4.0589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5501 3.0644 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.2016 2.1271 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.6309 1.3060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8739 0.6525 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9781 0.2079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.3070 -0.7365 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.0878 1.6638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1296 0.6647 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.9321 2.1996 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6544 4.0799 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2508 8.2431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3712 8.8557 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5940 7.7523 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2651 8.6967 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.5763 7.5649 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0103 5.7145 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9333 2.0419 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3632 -0.5826 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 57 1 0 0 0 0 3 4 1 0 0 0 0 4 5 2 3 0 0 0 4 70 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 6 0 0 0 6 8 1 0 0 0 0 8 9 2 3 0 0 0 8 69 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 1 0 0 0 10 15 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 14 1 0 0 0 0 15 16 2 3 0 0 0 15 68 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 65 1 1 0 0 0 18 19 1 0 0 0 0 19 20 2 3 0 0 0 19 64 1 0 0 0 0 20 21 1 0 0 0 0 21 22 1 1 0 0 0 21 29 1 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 26 28 1 0 0 0 0 29 30 2 3 0 0 0 29 63 1 0 0 0 0 30 31 1 0 0 0 0 31 32 1 1 0 0 0 31 49 1 0 0 0 0 32 33 2 0 0 0 0 33 34 1 0 0 0 0 34 35 2 0 0 0 0 34 48 1 0 0 0 0 35 36 1 0 0 0 0 36 37 1 6 0 0 0 36 38 1 0 0 0 0 38 39 1 1 0 0 0 38 46 1 0 0 0 0 39 40 1 0 0 0 0 40 45 2 0 0 0 0 40 41 1 0 0 0 0 41 42 2 0 0 0 0 42 43 1 0 0 0 0 43 44 2 0 0 0 0 44 45 1 0 0 0 0 46 47 1 0 0 0 0 49 50 1 6 0 0 0 49 51 1 0 0 0 0 51 52 2 3 0 0 0 51 62 1 0 0 0 0 52 53 1 0 0 0 0 53 54 1 0 0 0 0 53 59 1 1 0 0 0 54 55 1 0 0 0 0 55 56 1 0 0 0 0 56 57 2 3 0 0 0 56 58 1 0 0 0 0 59 60 2 0 0 0 0 59 61 1 0 0 0 0 65 66 2 0 0 0 0 65 67 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	980.53
Volume:	994.918
LogP:	0.905
LogD:	0.379
LogS:	-1.985
# Rotatable Bonds:	16
TPSA:	359.9
# H-Bond Aceptor:	22
# H-Bond Donor:	13
# Rings:	2
# Heavy Atoms:	22

MedChem Properties

QED Drug-Likeness Score:	0.04
Synthetic Accessibility Score:	6.697
Fsp3:	0.542
Lipinski Rule-of-5:	Rejected
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:	-7.02
MDCK Permeability:	8.451119356323034e-06
Pgp-inhibitor:	0.002
Pgp-substrate:	1.0
Human Intestinal Absorption (HIA):	0.8
20% Bioavailability (F20%):	0.522
30% Bioavailability (F30%):	0.977

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.33
Plasma Protein Binding (PPB):	31.93645477294922%
Volume Distribution (VD):	0.511
Pgp-substrate:	61.662628173828125%

ADMET: Metabolism

CYP1A2-inhibitor:	0.0
CYP1A2-substrate:	0.001
CYP2C19-inhibitor:	0.018
CYP2C19-substrate:	0.023
CYP2C9-inhibitor:	0.051
CYP2C9-substrate:	0.551
CYP2D6-inhibitor:	0.011
CYP2D6-substrate:	0.063
CYP3A4-inhibitor:	0.03
CYP3A4-substrate:	0.0

ADMET: Excretion

Clearance (CL):	1.622
Half-life (T1/2):	0.847

ADMET: Toxicity

hERG Blockers:	0.004
Human Hepatotoxicity (H-HT):	0.999
Drug-inuced Liver Injury (DILI):	0.907
AMES Toxicity:	0.078
Rat Oral Acute Toxicity:	0.04
Maximum Recommended Daily Dose:	0.9
Skin Sensitization:	0.633
Carcinogencity:	0.197
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.92

Download Data

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

Natural Product: NPC29679

Natural Product ID:	NPC29679
*Common Name:**	VDTOBYMILGRBLM-ZUCGMWCSSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VDTOBYMILGRBLM-ZUCGMWCSSA-N
Standard InCHI:	InChI=1S/C48H72N10O12/c1-9-32-43(63)52-30(7)42(62)57-36(22-26(2)3)45(65)58-37(47(68)69)25-40(60)54-34(16-13-21-51-48(49)50)44(64)55-33(29(6)41(61)56-35(46(66)67)19-20-39(59)53-32)18-17-27(4)23-28(5)38(70-8)24-31-14-11-10-12-15-31/h9-12,14-15,17-18,23,26,28-30,33-38H,13,16,19-22,24-25H2,1-8H3,(H,52,63)(H,53,59)(H,54,60)(H,55,64)(H,56,61)(H,57,62)(H,58,65)(H,66,67)(H,68,69)(H4,49,50,51)/b18-17+,27-23+,32-9+/t28-,29-,30+,33-,34-,35+,36-,37+,38-/m0/s1
SMILES:	C/C=C/1C(=N[C@H](C)C(=N[C@@H](CC(C)C)C(=N[C@H](CC(=N[C@@H](CCCNC(=N)N)C(=N[C@@H](/C=C/C(=C/[C@H](C)[C@H](Cc2ccccc2)OC)/C)[C@H](C)C(=N[C@H](CCC(=N1)O)C(=O)O)O)O)O)C(=O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	21637043
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0001813] Peptidomimetics [CHEMONTID:0002010] Hybrid peptides

*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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO15753	Pterocarpus angolensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11854	Romalea microptera	Species	Romaleidae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4232	Rabdosia coetsoides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16841	Elsholtzia bodinieri	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4232	Rabdosia coetsoides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12128	Ipomoea purpurea	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15753	Pterocarpus angolensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19977	Desmanthus illinoensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12128	Ipomoea purpurea	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO12128	Ipomoea purpurea	Species	Convolvulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9159	Narcissus serotinus	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4232	Rabdosia coetsoides	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11854	Romalea microptera	Species	Romaleidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15508	Ambrosia cordifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12412	Ormosia cinerea	Species	Limoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1443	Monomorium fieldi	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19977	Desmanthus illinoensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO911	Sistotrema raduloides	Species	Corticiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16841	Elsholtzia bodinieri	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14714	Equisetum silvaticum	Species	Equisetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15753	Pterocarpus angolensis	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16276	Croton hieronymi	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ 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

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ 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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC29679 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	142
0.1-0.2	764
0.2-0.3	3893
0.3-0.4	15003
0.4-0.5	18870
0.5-0.6	3252
0.6-0.7	650
0.7-0.8	117
0.8-0.85	2
0.85-0.9	1
0.9-0.95	3
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID

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 NPC29679 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	98
0.1-0.2	317
0.2-0.3	661
0.3-0.4	1692
0.4-0.5	4236
0.5-0.6	1929
0.6-0.7	204
0.7-0.8	13
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

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