Structure

Physi-Chem Properties

Molecular Weight:  297.25
Volume:  346.554
LogP:  5.878
LogD:  5.053
LogS:  -5.754
# Rotatable Bonds:  1
TPSA:  23.79
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  1

MedChem Properties

QED Drug-Likeness Score:  0.565
Synthetic Accessibility Score:  5.092
Fsp3:  0.762
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.677
MDCK Permeability:  2.942449282272719e-05
Pgp-inhibitor:  0.984
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.895
30% Bioavailability (F30%):  0.027

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.789
Plasma Protein Binding (PPB):  93.97454071044922%
Volume Distribution (VD):  2.515
Pgp-substrate:  6.428412914276123%

ADMET: Metabolism

CYP1A2-inhibitor:  0.938
CYP1A2-substrate:  0.683
CYP2C19-inhibitor:  0.449
CYP2C19-substrate:  0.836
CYP2C9-inhibitor:  0.276
CYP2C9-substrate:  0.061
CYP2D6-inhibitor:  0.028
CYP2D6-substrate:  0.041
CYP3A4-inhibitor:  0.91
CYP3A4-substrate:  0.452

ADMET: Excretion

Clearance (CL):  15.712
Half-life (T1/2):  0.18

ADMET: Toxicity

hERG Blockers:  0.186
Human Hepatotoxicity (H-HT):  0.764
Drug-inuced Liver Injury (DILI):  0.896
AMES Toxicity:  0.047
Rat Oral Acute Toxicity:  0.943
Maximum Recommended Daily Dose:  0.23
Skin Sensitization:  0.681
Carcinogencity:  0.541
Eye Corrosion:  0.913
Eye Irritation:  0.379
Respiratory Toxicity:  0.933

Download Data

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

  Natural Product: NPC474457

Natural Product ID:  NPC474457
Common Name*:   (1S,3Ar,3A1R,4S,6R,6As,9As)-1,4-Dimethyl-7-Methylene-6-(2-Methylprop-1-Enyl)Dodecahydro-1H-Phenalene-1-Carbonitrile
IUPAC Name:   (1S,3aR,4S,6R,6aS,9aS,9bR)-1,4-dimethyl-7-methylidene-6-(2-methylprop-1-enyl)-3,3a,4,5,6,6a,8,9,9a,9b-decahydro-2H-phenalene-1-carbonitrile
Synonyms:  
Standard InCHIKey:  FVLMFTXDYSOHDO-LGTVQRIOSA-N
Standard InCHI:  InChI=1S/C21H31N/c1-13(2)10-16-11-15(4)17-8-9-21(5,12-22)18-7-6-14(3)19(16)20(17)18/h10,15-20H,3,6-9,11H2,1-2,4-5H3/t15-,16-,17+,18-,19-,20+,21+/m0/s1
SMILES:  N#C[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:   CHEMBL469286
PubChem CID:   44566850
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
NPO30160 Cymbastela hooperi Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[19199790]
NPO30160 Cymbastela hooperi Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO30160 Cymbastela hooperi Species Axinellidae Eukaryota n.a. n.a. n.a. PMID[8759172]

☑ 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
NPT91 Cell Line KB Homo sapiens IC50 = 3.2 ug.mL-1 PMID[450840]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 0.0141 ug.mL-1 PMID[450840]
NPT2 Others Unspecified Ratio IC50 = 230.0 n.a. PMID[450840]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 0.0093 ug.mL-1 PMID[450840]
NPT2 Others Unspecified Ratio IC50 = 340.0 n.a. PMID[450840]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 31.0 nM PMID[450841]

☑ 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 NPC474457 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
0.9636 High Similarity NPC474420
0.9636 High Similarity NPC474454
0.9636 High Similarity NPC474455
0.963 High Similarity NPC475696
0.963 High Similarity NPC474415
0.963 High Similarity NPC474528
0.9286 High Similarity NPC475716
0.9245 High Similarity NPC474416
0.8679 High Similarity NPC476681
0.85 High Similarity NPC474086
0.8214 Intermediate Similarity NPC476679
0.8148 Intermediate Similarity NPC22765
0.7931 Intermediate Similarity NPC469770
0.7869 Intermediate Similarity NPC317778
0.7818 Intermediate Similarity NPC17518
0.7636 Intermediate Similarity NPC124851
0.7593 Intermediate Similarity NPC86683
0.7538 Intermediate Similarity NPC474456
0.7419 Intermediate Similarity NPC472827
0.7358 Intermediate Similarity NPC193180
0.7222 Intermediate Similarity NPC192529
0.7213 Intermediate Similarity NPC318036
0.7206 Intermediate Similarity NPC184919
0.7206 Intermediate Similarity NPC138409
0.7188 Intermediate Similarity NPC219621
0.717 Intermediate Similarity NPC103290
0.7097 Intermediate Similarity NPC173815
0.7091 Intermediate Similarity NPC202189
0.7049 Intermediate Similarity NPC123194
0.7037 Intermediate Similarity NPC105246
0.7037 Intermediate Similarity NPC190232
0.7031 Intermediate Similarity NPC311809
0.7 Intermediate Similarity NPC127944
0.6984 Remote Similarity NPC324944
0.6984 Remote Similarity NPC469769
0.6964 Remote Similarity NPC296337
0.6964 Remote Similarity NPC114239
0.6964 Remote Similarity NPC13991
0.6964 Remote Similarity NPC241784
0.6885 Remote Similarity NPC476683
0.6825 Remote Similarity NPC470369
0.6825 Remote Similarity NPC470370
0.6795 Remote Similarity NPC477289
0.6786 Remote Similarity NPC248411
0.6761 Remote Similarity NPC265789
0.6761 Remote Similarity NPC21773
0.6719 Remote Similarity NPC60772
0.6716 Remote Similarity NPC469662
0.6622 Remote Similarity NPC476308
0.6615 Remote Similarity NPC152211
0.6615 Remote Similarity NPC28755
0.6575 Remote Similarity NPC476904
0.6571 Remote Similarity NPC296697
0.6571 Remote Similarity NPC142754
0.6571 Remote Similarity NPC94192
0.6571 Remote Similarity NPC39157
0.6571 Remote Similarity NPC82477
0.6567 Remote Similarity NPC145715
0.6567 Remote Similarity NPC202118
0.6567 Remote Similarity NPC197238
0.6557 Remote Similarity NPC473728
0.6528 Remote Similarity NPC476329
0.6522 Remote Similarity NPC476039
0.6522 Remote Similarity NPC92327
0.6522 Remote Similarity NPC222366
0.6522 Remote Similarity NPC286669
0.6522 Remote Similarity NPC37792
0.6508 Remote Similarity NPC470893
0.65 Remote Similarity NPC200129
0.6479 Remote Similarity NPC286814
0.6471 Remote Similarity NPC473959
0.6429 Remote Similarity NPC176107
0.6429 Remote Similarity NPC197805
0.6429 Remote Similarity NPC220210
0.6429 Remote Similarity NPC20181
0.6418 Remote Similarity NPC469728
0.64 Remote Similarity NPC7214
0.6389 Remote Similarity NPC214770
0.6389 Remote Similarity NPC477856
0.6379 Remote Similarity NPC49088
0.6364 Remote Similarity NPC62086
0.6364 Remote Similarity NPC78551
0.6364 Remote Similarity NPC211322
0.6364 Remote Similarity NPC227632
0.6338 Remote Similarity NPC20610
0.6333 Remote Similarity NPC17810
0.6316 Remote Similarity NPC86538
0.6316 Remote Similarity NPC60556
0.6316 Remote Similarity NPC109813
0.6308 Remote Similarity NPC11130
0.6301 Remote Similarity NPC190035
0.6296 Remote Similarity NPC229262
0.6296 Remote Similarity NPC297643
0.6296 Remote Similarity NPC139717
0.6286 Remote Similarity NPC323005
0.6271 Remote Similarity NPC323445
0.6269 Remote Similarity NPC176621
0.625 Remote Similarity NPC139397
0.625 Remote Similarity NPC182815
0.625 Remote Similarity NPC472831
0.6232 Remote Similarity NPC169275
0.6232 Remote Similarity NPC52449
0.6216 Remote Similarity NPC474743
0.6216 Remote Similarity NPC474488
0.6212 Remote Similarity NPC472830
0.6197 Remote Similarity NPC193770
0.6176 Remote Similarity NPC60565
0.6164 Remote Similarity NPC475728
0.6164 Remote Similarity NPC159577
0.6164 Remote Similarity NPC265782
0.6164 Remote Similarity NPC2634
0.6164 Remote Similarity NPC307176
0.6164 Remote Similarity NPC40574
0.6164 Remote Similarity NPC260040
0.6164 Remote Similarity NPC251929
0.6164 Remote Similarity NPC282593
0.6164 Remote Similarity NPC35734
0.6143 Remote Similarity NPC163678
0.6143 Remote Similarity NPC268039
0.6143 Remote Similarity NPC107258
0.614 Remote Similarity NPC177470
0.6133 Remote Similarity NPC211641
0.6133 Remote Similarity NPC100334
0.6111 Remote Similarity NPC188292
0.6111 Remote Similarity NPC76145
0.6111 Remote Similarity NPC160209
0.6111 Remote Similarity NPC34764
0.6111 Remote Similarity NPC216460
0.6111 Remote Similarity NPC310992
0.6111 Remote Similarity NPC260474
0.6111 Remote Similarity NPC32055
0.6111 Remote Similarity NPC190810
0.6087 Remote Similarity NPC283247
0.6081 Remote Similarity NPC470078
0.6081 Remote Similarity NPC115023
0.6081 Remote Similarity NPC225467
0.6081 Remote Similarity NPC54123
0.6076 Remote Similarity NPC12035
0.6056 Remote Similarity NPC279434
0.6056 Remote Similarity NPC259156
0.6056 Remote Similarity NPC149680
0.6056 Remote Similarity NPC242945
0.6056 Remote Similarity NPC185587
0.6056 Remote Similarity NPC176171
0.6053 Remote Similarity NPC293803
0.6053 Remote Similarity NPC125828
0.6029 Remote Similarity NPC127582
0.6027 Remote Similarity NPC476431
0.6 Remote Similarity NPC303613
0.6 Remote Similarity NPC329782
0.6 Remote Similarity NPC118329
0.6 Remote Similarity NPC285371
0.6 Remote Similarity NPC475124
0.6 Remote Similarity NPC474228
0.6 Remote Similarity NPC182717
0.6 Remote Similarity NPC152039
0.6 Remote Similarity NPC476682
0.6 Remote Similarity NPC471799
0.6 Remote Similarity NPC251705
0.5974 Remote Similarity NPC470749
0.5974 Remote Similarity NPC120098
0.5974 Remote Similarity NPC237460
0.5974 Remote Similarity NPC30590
0.5974 Remote Similarity NPC122418
0.5974 Remote Similarity NPC290598
0.5974 Remote Similarity NPC265328
0.5974 Remote Similarity NPC106364
0.5974 Remote Similarity NPC112680
0.5974 Remote Similarity NPC27765
0.5972 Remote Similarity NPC68703
0.5972 Remote Similarity NPC476135
0.5972 Remote Similarity NPC69649
0.5965 Remote Similarity NPC144023
0.5946 Remote Similarity NPC145498
0.5926 Remote Similarity NPC215474
0.5926 Remote Similarity NPC283277
0.5926 Remote Similarity NPC92224
0.5926 Remote Similarity NPC472312
0.5921 Remote Similarity NPC219232
0.5921 Remote Similarity NPC241854
0.5921 Remote Similarity NPC471797
0.5921 Remote Similarity NPC476046
0.5921 Remote Similarity NPC128346
0.5921 Remote Similarity NPC251970
0.5915 Remote Similarity NPC476737
0.5915 Remote Similarity NPC27243
0.5909 Remote Similarity NPC264779
0.5897 Remote Similarity NPC249018
0.5897 Remote Similarity NPC91665
0.5897 Remote Similarity NPC470751
0.5897 Remote Similarity NPC157996
0.5897 Remote Similarity NPC40394
0.5897 Remote Similarity NPC107039
0.5897 Remote Similarity NPC3190
0.5897 Remote Similarity NPC470711
0.5897 Remote Similarity NPC101475
0.5897 Remote Similarity NPC470750
0.5897 Remote Similarity NPC90979
0.5897 Remote Similarity NPC472805
0.5897 Remote Similarity NPC471897

  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 NPC474457 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
0.7037 Intermediate Similarity NPD1799 Clinical (unspecified phase)
0.6857 Remote Similarity NPD6939 Phase 2
0.6857 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6842 Remote Similarity NPD8028 Phase 2
0.6338 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6333 Remote Similarity NPD8262 Approved
0.625 Remote Similarity NPD4137 Phase 3
0.6164 Remote Similarity NPD4691 Approved
0.6164 Remote Similarity NPD4747 Approved
0.6111 Remote Similarity NPD319 Phase 1
0.6081 Remote Similarity NPD4243 Approved
0.5921 Remote Similarity NPD4058 Approved
0.5921 Remote Similarity NPD4784 Approved
0.5921 Remote Similarity NPD4785 Approved
0.5867 Remote Similarity NPD5365 Phase 2
0.5844 Remote Similarity NPD6942 Approved
0.5844 Remote Similarity NPD5275 Approved
0.5844 Remote Similarity NPD7339 Approved
0.5844 Remote Similarity NPD4190 Phase 3
0.5783 Remote Similarity NPD4544 Approved
0.5778 Remote Similarity NPD7732 Phase 3
0.5778 Remote Similarity NPD7614 Phase 1
0.5769 Remote Similarity NPD3701 Clinical (unspecified phase)
0.575 Remote Similarity NPD7645 Phase 2
0.5747 Remote Similarity NPD4096 Approved
0.5714 Remote Similarity NPD5733 Approved
0.5714 Remote Similarity NPD4687 Approved
0.5679 Remote Similarity NPD7525 Registered
0.5663 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5658 Remote Similarity NPD5276 Approved
0.56 Remote Similarity NPD6922 Approved
0.56 Remote Similarity NPD6923 Approved

  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