Structure

Physi-Chem Properties

Molecular Weight:  315.26
Volume:  357.98
LogP:  5.487
LogD:  4.915
LogS:  -4.056
# Rotatable Bonds:  3
TPSA:  29.1
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.592
Synthetic Accessibility Score:  5.178
Fsp3:  0.762
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.592
MDCK Permeability:  2.202348150603939e-05
Pgp-inhibitor:  0.006
Pgp-substrate:  0.039
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.9
30% Bioavailability (F30%):  0.026

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.68
Plasma Protein Binding (PPB):  78.9528579711914%
Volume Distribution (VD):  2.107
Pgp-substrate:  8.732575416564941%

ADMET: Metabolism

CYP1A2-inhibitor:  0.911
CYP1A2-substrate:  0.596
CYP2C19-inhibitor:  0.801
CYP2C19-substrate:  0.879
CYP2C9-inhibitor:  0.124
CYP2C9-substrate:  0.085
CYP2D6-inhibitor:  0.025
CYP2D6-substrate:  0.431
CYP3A4-inhibitor:  0.747
CYP3A4-substrate:  0.386

ADMET: Excretion

Clearance (CL):  12.045
Half-life (T1/2):  0.144

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.717
Drug-inuced Liver Injury (DILI):  0.292
AMES Toxicity:  0.1
Rat Oral Acute Toxicity:  0.929
Maximum Recommended Daily Dose:  0.044
Skin Sensitization:  0.61
Carcinogencity:  0.673
Eye Corrosion:  0.006
Eye Irritation:  0.025
Respiratory Toxicity:  0.939

Download Data

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

  Natural Product: NPC476329

Natural Product ID:  NPC476329
Common Name*:   (1R*,3S*,4R*,7S*,8S*,12S*,13S*)-7-Formamidoamphilecta-11(20),14-Diene
IUPAC Name:   N-[(1S,3aR,4S,6R,6aS,9aS,9bS)-1,4-dimethyl-7-methylidene-6-(2-methylprop-1-enyl)-3,3a,4,5,6,6a,8,9,9a,9b-decahydro-2H-phenalen-1-yl]formamide
Synonyms:  
Standard InCHIKey:  JGPUUJQGPXIAOU-QQKCOMIHSA-N
Standard InCHI:  InChI=1S/C21H33NO/c1-13(2)10-16-11-15(4)17-8-9-21(5,22-12-23)18-7-6-14(3)19(16)20(17)18/h10,12,15-20H,3,6-9,11H2,1-2,4-5H3,(H,22,23)/t15-,16-,17+,18-,19-,20+,21-/m0/s1
SMILES:  OC=N[C@@]1(C)CC[C@H]2[C@@H]3[C@@H]1CCC(=C)[C@H]3[C@H](C[C@@H]2C)C=C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL565148
PubChem CID:   10925113
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003398] Amphilectane, neoamphilectane, cycloamphilectane, and adociane diterpenoids

*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
NPO33434 cymbastel hooperi Species n.a. n.a. n.a. n.a. n.a. PMID[19199790]

☑ 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
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 63.0 ug.mL-1 PMID[501130]

☑ 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 NPC476329 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.9429 High Similarity NPC476308
0.9394 High Similarity NPC476135
0.8382 Intermediate Similarity NPC476682
0.831 Intermediate Similarity NPC138409
0.8209 Intermediate Similarity NPC317778
0.7808 Intermediate Similarity NPC184919
0.7808 Intermediate Similarity NPC472831
0.7714 Intermediate Similarity NPC89921
0.7714 Intermediate Similarity NPC145715
0.7647 Intermediate Similarity NPC324944
0.7612 Intermediate Similarity NPC318036
0.7606 Intermediate Similarity NPC473959
0.75 Intermediate Similarity NPC173815
0.7246 Intermediate Similarity NPC470370
0.7246 Intermediate Similarity NPC470369
0.72 Intermediate Similarity NPC476288
0.7176 Intermediate Similarity NPC474458
0.7059 Intermediate Similarity NPC152684
0.7042 Intermediate Similarity NPC28755
0.7042 Intermediate Similarity NPC152211
0.6944 Remote Similarity NPC311809
0.6933 Remote Similarity NPC37792
0.6849 Remote Similarity NPC219621
0.6786 Remote Similarity NPC475724
0.6757 Remote Similarity NPC477740
0.675 Remote Similarity NPC476904
0.6711 Remote Similarity NPC474456
0.6709 Remote Similarity NPC21773
0.6667 Remote Similarity NPC124384
0.6667 Remote Similarity NPC250632
0.6622 Remote Similarity NPC477739
0.6591 Remote Similarity NPC166458
0.6588 Remote Similarity NPC257962
0.6548 Remote Similarity NPC211322
0.6528 Remote Similarity NPC474457
0.6512 Remote Similarity NPC283277
0.65 Remote Similarity NPC265789
0.6494 Remote Similarity NPC476039
0.6494 Remote Similarity NPC286669
0.6494 Remote Similarity NPC222366
0.6452 Remote Similarity NPC243985
0.6452 Remote Similarity NPC280710
0.641 Remote Similarity NPC197805
0.6404 Remote Similarity NPC157479
0.6386 Remote Similarity NPC7214
0.6351 Remote Similarity NPC474455
0.6351 Remote Similarity NPC472827
0.6351 Remote Similarity NPC474420
0.6351 Remote Similarity NPC474454
0.6324 Remote Similarity NPC22765
0.6322 Remote Similarity NPC215474
0.6316 Remote Similarity NPC474027
0.6316 Remote Similarity NPC474435
0.6316 Remote Similarity NPC476903
0.6301 Remote Similarity NPC475696
0.6301 Remote Similarity NPC11130
0.6301 Remote Similarity NPC474528
0.6301 Remote Similarity NPC474415
0.63 Remote Similarity NPC55462
0.6292 Remote Similarity NPC24733
0.6292 Remote Similarity NPC311769
0.6292 Remote Similarity NPC147513
0.6292 Remote Similarity NPC182106
0.6286 Remote Similarity NPC212905
0.6277 Remote Similarity NPC477290
0.6265 Remote Similarity NPC125828
0.6264 Remote Similarity NPC259252
0.6263 Remote Similarity NPC474583
0.625 Remote Similarity NPC469770
0.625 Remote Similarity NPC167419
0.625 Remote Similarity NPC240650
0.6235 Remote Similarity NPC79704
0.6222 Remote Similarity NPC56107
0.622 Remote Similarity NPC474743
0.6207 Remote Similarity NPC329782
0.6162 Remote Similarity NPC471083
0.6154 Remote Similarity NPC163678
0.6145 Remote Similarity NPC100334
0.6136 Remote Similarity NPC224072
0.6136 Remote Similarity NPC472312
0.6133 Remote Similarity NPC475716
0.6125 Remote Similarity NPC94192
0.6125 Remote Similarity NPC216460
0.6125 Remote Similarity NPC32055
0.6125 Remote Similarity NPC160209
0.6111 Remote Similarity NPC75810
0.6092 Remote Similarity NPC12035
0.6087 Remote Similarity NPC324405
0.6087 Remote Similarity NPC17518
0.6082 Remote Similarity NPC184033
0.6078 Remote Similarity NPC25340
0.6076 Remote Similarity NPC149680
0.6067 Remote Similarity NPC171639
0.6067 Remote Similarity NPC21667
0.6058 Remote Similarity NPC472359
0.6049 Remote Similarity NPC245223
0.6042 Remote Similarity NPC272732
0.6042 Remote Similarity NPC311164
0.6024 Remote Similarity NPC471799
0.6024 Remote Similarity NPC182717
0.6023 Remote Similarity NPC152039
0.6023 Remote Similarity NPC118329
0.6022 Remote Similarity NPC249312
0.6 Remote Similarity NPC470749
0.6 Remote Similarity NPC265328
0.6 Remote Similarity NPC69649
0.6 Remote Similarity NPC120098
0.6 Remote Similarity NPC68703
0.6 Remote Similarity NPC106364
0.6 Remote Similarity NPC122418
0.6 Remote Similarity NPC290598
0.6 Remote Similarity NPC247060
0.6 Remote Similarity NPC27765
0.6 Remote Similarity NPC237460
0.6 Remote Similarity NPC50815
0.6 Remote Similarity NPC476752
0.6 Remote Similarity NPC476753
0.6 Remote Similarity NPC30590
0.5976 Remote Similarity NPC472543
0.5976 Remote Similarity NPC145498
0.5972 Remote Similarity NPC474416
0.596 Remote Similarity NPC275686
0.5955 Remote Similarity NPC39966
0.5952 Remote Similarity NPC471797
0.5949 Remote Similarity NPC27243
0.5949 Remote Similarity NPC476737
0.5942 Remote Similarity NPC124851
0.5941 Remote Similarity NPC241879
0.5941 Remote Similarity NPC293299
0.5941 Remote Similarity NPC45365
0.5938 Remote Similarity NPC476754
0.593 Remote Similarity NPC90979
0.593 Remote Similarity NPC472805
0.593 Remote Similarity NPC470758
0.593 Remote Similarity NPC470711
0.593 Remote Similarity NPC157996
0.593 Remote Similarity NPC101475
0.593 Remote Similarity NPC40394
0.593 Remote Similarity NPC34177
0.5926 Remote Similarity NPC208999
0.5918 Remote Similarity NPC140300
0.5918 Remote Similarity NPC474164
0.5914 Remote Similarity NPC34754
0.5904 Remote Similarity NPC242001
0.5904 Remote Similarity NPC167706
0.5897 Remote Similarity NPC475755
0.5882 Remote Similarity NPC136188
0.5882 Remote Similarity NPC471723
0.5882 Remote Similarity NPC230301
0.5882 Remote Similarity NPC34700
0.5882 Remote Similarity NPC162742
0.5882 Remote Similarity NPC141071
0.5882 Remote Similarity NPC257347
0.5882 Remote Similarity NPC22105
0.5882 Remote Similarity NPC288035
0.5882 Remote Similarity NPC138374
0.5882 Remote Similarity NPC134847
0.5882 Remote Similarity NPC28657
0.5882 Remote Similarity NPC304309
0.5882 Remote Similarity NPC119329
0.5882 Remote Similarity NPC285893
0.5875 Remote Similarity NPC250977
0.5862 Remote Similarity NPC158662
0.5862 Remote Similarity NPC85346
0.5862 Remote Similarity NPC244385
0.5862 Remote Similarity NPC470396
0.5862 Remote Similarity NPC230295
0.5862 Remote Similarity NPC302041
0.5862 Remote Similarity NPC6978
0.5862 Remote Similarity NPC196753
0.5862 Remote Similarity NPC285761
0.5862 Remote Similarity NPC474989
0.5862 Remote Similarity NPC138621
0.5862 Remote Similarity NPC253807
0.5862 Remote Similarity NPC300499
0.5862 Remote Similarity NPC65897
0.5862 Remote Similarity NPC312328
0.5862 Remote Similarity NPC22955
0.5862 Remote Similarity NPC99168
0.5862 Remote Similarity NPC167037
0.5862 Remote Similarity NPC98386
0.5859 Remote Similarity NPC91604
0.5859 Remote Similarity NPC140685
0.5844 Remote Similarity NPC176621
0.5843 Remote Similarity NPC90150
0.5842 Remote Similarity NPC152718
0.5842 Remote Similarity NPC226509
0.5814 Remote Similarity NPC134330
0.5814 Remote Similarity NPC189883
0.5814 Remote Similarity NPC321381
0.5814 Remote Similarity NPC107059
0.5814 Remote Similarity NPC244488
0.5814 Remote Similarity NPC321016
0.5814 Remote Similarity NPC113733
0.5814 Remote Similarity NPC247325
0.5814 Remote Similarity NPC300324
0.5814 Remote Similarity NPC129165
0.5814 Remote Similarity NPC240604
0.5795 Remote Similarity NPC291379
0.5795 Remote Similarity NPC273410

  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 NPC476329 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.65 Remote Similarity NPD5365 Phase 2
0.6452 Remote Similarity NPD5771 Approved
0.6375 Remote Similarity NPD6939 Phase 2
0.6375 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6277 Remote Similarity NPD5769 Clinical (unspecified phase)
0.6146 Remote Similarity NPD2895 Discontinued
0.604 Remote Similarity NPD7812 Clinical (unspecified phase)
0.5882 Remote Similarity NPD7339 Approved
0.5882 Remote Similarity NPD6942 Approved
0.5795 Remote Similarity NPD7645 Phase 2
0.573 Remote Similarity NPD7525 Registered
0.5714 Remote Similarity NPD4243 Approved
0.5663 Remote Similarity NPD6923 Approved
0.5663 Remote Similarity NPD6922 Approved
0.5632 Remote Similarity NPD3701 Clinical (unspecified phase)

  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