NPASS Compound

Structure

NPC473640 OpenBabel07101719142D 55 58 0 0 1 0 0 0 0 0999 V2000 -3.5234 8.4762 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1071 7.4792 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6681 5.5149 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3306 5.0292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1588 -0.8551 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2183 0.5151 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0998 6.6946 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4036 4.9653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4036 5.9653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4013 -0.8090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5376 4.4653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5376 6.4653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6092 0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4067 -0.9135 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6787 6.7511 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0787 3.8322 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4115 3.7052 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1327 5.4653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9133 -1.5545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1031 7.5688 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3591 4.7921 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2930 0.1359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3475 5.8002 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.7205 4.6562 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6715 4.9653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6715 5.9653 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2583 5.8438 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1072 3.5951 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4333 3.4973 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8983 -0.5546 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.7431 0.6691 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5020 0.7476 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2986 6.1092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0819 4.4335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0929 5.2929 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1969 2.5992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2560 1.5276 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7792 0.0565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9074 -0.4204 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7205 6.2743 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 0.4702 5.2246 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.2984 6.1242 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.7280 4.5204 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 1.4931 2.4991 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.8848 -0.3908 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -4.9890 1.6210 0.0000 N 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 -1.0548 -2.0674 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1347 7.0957 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9554 4.9205 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7620 6.0360 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.1951 2.5394 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1813 1.1484 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3548 -0.7612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6269 -1.3802 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 20 1 0 0 0 0 2 20 1 0 0 0 0 3 21 1 0 0 0 0 4 21 1 0 0 0 0 5 22 1 0 0 0 0 6 22 1 0 0 0 0 8 9 2 0 0 0 0 8 11 1 0 0 0 0 9 12 1 0 0 0 0 10 13 1 0 0 0 0 10 14 1 0 0 0 0 11 25 2 0 0 0 0 12 26 2 0 0 0 0 14 47 1 0 0 0 0 15 20 1 0 0 0 0 16 21 1 0 0 0 0 17 24 1 0 0 0 0 18 24 2 0 0 0 0 18 40 1 0 0 0 0 19 48 1 0 0 0 0 23 7 1 6 0 0 0 23 33 1 0 0 0 0 23 41 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 40 1 0 0 0 0 27 15 1 6 0 0 0 27 35 1 0 0 0 0 27 42 1 0 0 0 0 28 16 1 6 0 0 0 28 36 1 0 0 0 0 28 43 1 0 0 0 0 29 17 1 6 0 0 0 29 34 1 0 0 0 0 29 44 1 0 0 0 0 30 19 1 6 0 0 0 30 39 1 0 0 0 0 30 45 1 0 0 0 0 31 13 1 6 0 0 0 31 37 1 0 0 0 0 31 47 1 0 0 0 0 32 22 1 6 0 0 0 32 38 1 0 0 0 0 32 46 1 0 0 0 0 33 42 2 3 0 0 0 33 49 1 0 0 0 0 34 41 2 3 0 0 0 34 50 1 0 0 0 0 35 43 2 3 0 0 0 35 51 1 0 0 0 0 36 46 2 3 0 0 0 36 52 1 0 0 0 0 37 44 2 3 0 0 0 37 53 1 0 0 0 0 38 45 2 3 0 0 0 38 54 1 0 0 0 0 39 47 1 0 0 0 0 39 55 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	766.44
Volume:	778.169
LogP:	2.419
LogD:	3.218
LogS:	-3.165
# Rotatable Bonds:	8
TPSA:	237.91
# H-Bond Aceptor:	16
# H-Bond Donor:	8
# Rings:	4
# Heavy Atoms:	16

MedChem Properties

QED Drug-Likeness Score:	0.198
Synthetic Accessibility Score:	5.634
Fsp3:	0.615
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:	-5.327
MDCK Permeability:	2.1420029952423647e-05
Pgp-inhibitor:	0.57
Pgp-substrate:	0.999
Human Intestinal Absorption (HIA):	0.377
20% Bioavailability (F20%):	0.996
30% Bioavailability (F30%):	0.117

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.058
Plasma Protein Binding (PPB):	37.19786071777344%
Volume Distribution (VD):	0.556
Pgp-substrate:	41.955467224121094%

ADMET: Metabolism

CYP1A2-inhibitor:	0.004
CYP1A2-substrate:	0.004
CYP2C19-inhibitor:	0.041
CYP2C19-substrate:	0.044
CYP2C9-inhibitor:	0.024
CYP2C9-substrate:	0.594
CYP2D6-inhibitor:	0.085
CYP2D6-substrate:	0.093
CYP3A4-inhibitor:	0.138
CYP3A4-substrate:	0.037

ADMET: Excretion

Clearance (CL):	1.51
Half-life (T1/2):	0.892

ADMET: Toxicity

hERG Blockers:	0.002
Human Hepatotoxicity (H-HT):	0.997
Drug-inuced Liver Injury (DILI):	0.964
AMES Toxicity:	0.004
Rat Oral Acute Toxicity:	0.307
Maximum Recommended Daily Dose:	0.834
Skin Sensitization:	0.153
Carcinogencity:	0.105
Eye Corrosion:	0.003
Eye Irritation:	0.006
Respiratory Toxicity:	0.911

Download Data

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

Natural Product: NPC473640

Natural Product ID:	NPC473640
*Common Name:**	Integerrimide B
IUPAC Name:	(3S,6S,9S,12S,15S,18S,21S)-3-(hydroxymethyl)-18-(1H-indol-3-ylmethyl)-15-methyl-9,12-bis(2-methylpropyl)-6-propan-2-yl-1,4,7,10,13,16,19-heptazabicyclo[19.3.0]tetracosane-2,5,8,11,14,17,20-heptone
Synonyms:
Standard InCHIKey:	WFQBWZPTVRKYLS-HVEPFCGMSA-N
Standard InCHI:	InChI=1S/C39H58N8O8/c1-20(2)15-27-35(51)43-28(16-21(3)4)36(52)46-32(22(5)6)38(54)45-30(19-48)39(55)47-14-10-13-31(47)37(53)44-29(34(50)41-23(7)33(49)42-27)17-24-18-40-26-12-9-8-11-25(24)26/h8-9,11-12,18,20-23,27-32,40,48H,10,13-17,19H2,1-7H3,(H,41,50)(H,42,49)(H,43,51)(H,44,53)(H,45,54)(H,46,52)/t23-,27-,28-,29-,30-,31-,32-/m0/s1
SMILES:	CC1C(=O)NC(C(=O)NC(C(=O)NC(C(=O)NC(C(=O)N2CCCC2C(=O)NC(C(=O)N1)CC3=CNC4=CC=CC=C43)CO)C(C)C)CC(C)C)CC(C)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL447891
PubChem CID:	16059804
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000264] Organic acids and derivatives [CHEMONTID:0000265] Carboxylic acids and derivatives [CHEMONTID:0000013] Amino acids, peptides, and analogues [CHEMONTID:0000348] Peptides [CHEMONTID:0004831] Oligopeptides

*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

Show entries

Search:

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO19811	Jatropha integerrima	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19943622]
NPO19811	Jatropha integerrima	Species	Euphorbiaceae	Eukaryota	latex	n.a.	n.a.	PMID[17067157]
NPO19811	Jatropha integerrima	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Showing 1 to 3 of 3 entries

Previous1Next

☑ 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

Show entries

Search:

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

Showing 0 to 0 of 0 entries

PreviousNext

☑ 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
Others	2

Activity Type	# Activity
Cell Line	2

Show entries

Search:

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT4617	Cell Line	IPC-298	Homo sapiens	Activity	=	40.0	%	PMID[465774]
NPT1313	Cell Line	Capan-2	Homo sapiens	Inhibition	=	20.0	%	PMID[465774]

Showing 1 to 2 of 2 entries

Previous1Next

☑ 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 NPC473640 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	289
0.1-0.2	2023
0.2-0.3	17511
0.3-0.4	15214
0.4-0.5	2801
0.5-0.6	2728
0.6-0.7	1456
0.7-0.8	550
0.8-0.85	72
0.85-0.9	40
0.9-0.95	9
0.95-1	4

Show entries

Search:

Similarity Score	Similarity Level	Natural Product ID
0.9831	High Similarity	NPC475506
0.9777	High Similarity	NPC155143
0.9609	High Similarity	NPC100321
0.9459	High Similarity	NPC223791
0.9459	High Similarity	NPC107077

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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 NPC473640 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	172
0.1-0.2	485
0.2-0.3	969
0.3-0.4	1665
0.4-0.5	2555
0.5-0.6	2333
0.6-0.7	831
0.7-0.8	117
0.8-0.85	21
0.85-0.9	1
0.9-0.95	1
0.95-1	0

Show entries

Search:

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.914	High Similarity	NPD8272	Phase 2
0.9076	High Similarity	NPD7621	Clinical (unspecified phase)
0.8842	High Similarity	NPD8493	Clinical (unspecified phase)
0.8427	Intermediate Similarity	NPD4184	Clinical (unspecified phase)
0.8418	Intermediate Similarity	NPD7809	Clinical (unspecified phase)

Showing 1 to 5 of 200 entries

Previous1 2 3 4 5…40Next

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