Structure

Physi-Chem Properties

Molecular Weight:  297.25
Volume:  346.554
LogP:  6.52
LogD:  5.078
LogS:  -5.632
# 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:  5.089
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:  -4.62
MDCK Permeability:  2.9426722903735936e-05
Pgp-inhibitor:  0.991
Pgp-substrate:  0.053
Human Intestinal Absorption (HIA):  0.007
20% Bioavailability (F20%):  0.898
30% Bioavailability (F30%):  0.032

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.359
Plasma Protein Binding (PPB):  93.42179107666016%
Volume Distribution (VD):  4.957
Pgp-substrate:  4.591460227966309%

ADMET: Metabolism

CYP1A2-inhibitor:  0.942
CYP1A2-substrate:  0.641
CYP2C19-inhibitor:  0.524
CYP2C19-substrate:  0.823
CYP2C9-inhibitor:  0.277
CYP2C9-substrate:  0.045
CYP2D6-inhibitor:  0.042
CYP2D6-substrate:  0.035
CYP3A4-inhibitor:  0.905
CYP3A4-substrate:  0.474

ADMET: Excretion

Clearance (CL):  18.6
Half-life (T1/2):  0.153

ADMET: Toxicity

hERG Blockers:  0.215
Human Hepatotoxicity (H-HT):  0.87
Drug-inuced Liver Injury (DILI):  0.886
AMES Toxicity:  0.078
Rat Oral Acute Toxicity:  0.967
Maximum Recommended Daily Dose:  0.065
Skin Sensitization:  0.912
Carcinogencity:  0.535
Eye Corrosion:  0.97
Eye Irritation:  0.723
Respiratory Toxicity:  0.958

Download Data

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

  Natural Product: NPC474528

Natural Product ID:  NPC474528
Common Name*:   (1R*,3S*,4R*,7S*,8S*,12S*,13S*)-7-Isocyanoamphilecta-10,14-Diene
IUPAC Name:   (1S,3aR,4S,6R,6aS,9aS,9bS)-1,4,7-trimethyl-6-(2-methylprop-1-enyl)-2,3,3a,4,5,6,6a,9,9a,9b-decahydrophenalene-1-carbonitrile
Synonyms:  
Standard InCHIKey:  SUQFWVZYUFDVKT-QGVNFLHTSA-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/h6,10,15-20H,7-9,11H2,1-5H3/t15-,16-,17+,18-,19-,20-,21+/m0/s1
SMILES:  N#C[C@@]1(C)CC[C@H]2[C@H]3[C@@H]1CC=C([C@H]3[C@H](C[C@@H]2C)C=C(C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL471077
PubChem CID:   44559504
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
NPO33096 stylissa sp. Species Axinellidae Eukaryota n.a. Okinawan n.a. PMID[15165146]

☑ 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
NPT165 Cell Line HeLa Homo sapiens IC50 = 20000.0 nM PMID[458655]

☑ 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 NPC474528 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
1.0 High Similarity NPC474415
1.0 High Similarity NPC475696
0.9636 High Similarity NPC474420
0.9636 High Similarity NPC475716
0.9636 High Similarity NPC474454
0.9636 High Similarity NPC474455
0.963 High Similarity NPC474457
0.8889 High Similarity NPC474416
0.8679 High Similarity NPC476681
0.85 High Similarity NPC474086
0.8214 Intermediate Similarity NPC476679
0.8148 Intermediate Similarity NPC22765
0.8148 Intermediate Similarity NPC17518
0.7931 Intermediate Similarity NPC469770
0.7925 Intermediate Similarity NPC86683
0.7636 Intermediate Similarity NPC124851
0.7581 Intermediate Similarity NPC317778
0.7547 Intermediate Similarity NPC192529
0.7419 Intermediate Similarity NPC472827
0.7407 Intermediate Similarity NPC202189
0.7358 Intermediate Similarity NPC193180
0.7333 Intermediate Similarity NPC123194
0.7302 Intermediate Similarity NPC311809
0.7273 Intermediate Similarity NPC13991
0.7273 Intermediate Similarity NPC296337
0.7273 Intermediate Similarity NPC241784
0.7273 Intermediate Similarity NPC474456
0.7273 Intermediate Similarity NPC114239
0.7258 Intermediate Similarity NPC469769
0.7206 Intermediate Similarity NPC184919
0.7206 Intermediate Similarity NPC138409
0.7188 Intermediate Similarity NPC219621
0.717 Intermediate Similarity NPC103290
0.7097 Intermediate Similarity NPC470370
0.7097 Intermediate Similarity NPC470369
0.7091 Intermediate Similarity NPC248411
0.7037 Intermediate Similarity NPC190232
0.7037 Intermediate Similarity NPC105246
0.7 Intermediate Similarity NPC21773
0.7 Intermediate Similarity NPC265789
0.697 Remote Similarity NPC469662
0.6935 Remote Similarity NPC318036
0.6885 Remote Similarity NPC476683
0.6833 Remote Similarity NPC473728
0.6825 Remote Similarity NPC173815
0.6818 Remote Similarity NPC202118
0.6818 Remote Similarity NPC197238
0.6818 Remote Similarity NPC145715
0.6806 Remote Similarity NPC476904
0.6795 Remote Similarity NPC477289
0.678 Remote Similarity NPC200129
0.6774 Remote Similarity NPC470893
0.6765 Remote Similarity NPC286669
0.6765 Remote Similarity NPC222366
0.6765 Remote Similarity NPC92327
0.6765 Remote Similarity NPC476039
0.6721 Remote Similarity NPC127944
0.6719 Remote Similarity NPC60772
0.6719 Remote Similarity NPC324944
0.6716 Remote Similarity NPC473959
0.6667 Remote Similarity NPC469728
0.6667 Remote Similarity NPC176107
0.6667 Remote Similarity NPC197805
0.6622 Remote Similarity NPC476308
0.6622 Remote Similarity NPC7214
0.6615 Remote Similarity NPC152211
0.6615 Remote Similarity NPC28755
0.661 Remote Similarity NPC17810
0.6604 Remote Similarity NPC229262
0.6604 Remote Similarity NPC139717
0.6604 Remote Similarity NPC297643
0.6571 Remote Similarity NPC296697
0.6571 Remote Similarity NPC142754
0.6571 Remote Similarity NPC39157
0.6571 Remote Similarity NPC20610
0.6571 Remote Similarity NPC82477
0.6522 Remote Similarity NPC323005
0.6522 Remote Similarity NPC37792
0.6479 Remote Similarity NPC182815
0.6479 Remote Similarity NPC286814
0.6479 Remote Similarity NPC139397
0.6429 Remote Similarity NPC193770
0.6429 Remote Similarity NPC220210
0.6429 Remote Similarity NPC20181
0.6429 Remote Similarity NPC177470
0.6415 Remote Similarity NPC34764
0.6415 Remote Similarity NPC190810
0.6415 Remote Similarity NPC76145
0.6389 Remote Similarity NPC260040
0.6389 Remote Similarity NPC282593
0.6389 Remote Similarity NPC265782
0.6389 Remote Similarity NPC251929
0.6389 Remote Similarity NPC2634
0.6389 Remote Similarity NPC35734
0.6389 Remote Similarity NPC475728
0.6389 Remote Similarity NPC159577
0.6389 Remote Similarity NPC307176
0.6379 Remote Similarity NPC49088
0.6377 Remote Similarity NPC163678
0.6364 Remote Similarity NPC62086
0.6364 Remote Similarity NPC78551
0.6364 Remote Similarity NPC227632
0.6338 Remote Similarity NPC32055
0.6338 Remote Similarity NPC188292
0.6338 Remote Similarity NPC94192
0.6338 Remote Similarity NPC216460
0.6338 Remote Similarity NPC260474
0.6338 Remote Similarity NPC310992
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
0.6301 Remote Similarity NPC470078
0.6301 Remote Similarity NPC54123
0.6301 Remote Similarity NPC115023
0.6301 Remote Similarity NPC476329
0.6286 Remote Similarity NPC242945
0.6286 Remote Similarity NPC279434
0.6286 Remote Similarity NPC259156
0.6286 Remote Similarity NPC176171
0.6282 Remote Similarity NPC12035
0.6271 Remote Similarity NPC323445
0.6269 Remote Similarity NPC176621
0.6269 Remote Similarity NPC127582
0.6267 Remote Similarity NPC125828
0.625 Remote Similarity NPC144023
0.625 Remote Similarity NPC472831
0.6232 Remote Similarity NPC475124
0.6232 Remote Similarity NPC285371
0.6232 Remote Similarity NPC169275
0.6232 Remote Similarity NPC52449
0.6216 Remote Similarity NPC474488
0.6216 Remote Similarity NPC474228
0.6216 Remote Similarity NPC471799
0.6216 Remote Similarity NPC303613
0.6216 Remote Similarity NPC182717
0.6216 Remote Similarity NPC251705
0.6212 Remote Similarity NPC472830
0.6203 Remote Similarity NPC329782
0.6203 Remote Similarity NPC152039
0.6203 Remote Similarity NPC118329
0.6176 Remote Similarity NPC60565
0.6164 Remote Similarity NPC477856
0.6164 Remote Similarity NPC214770
0.6164 Remote Similarity NPC145498
0.6154 Remote Similarity NPC211322
0.6143 Remote Similarity NPC268039
0.6143 Remote Similarity NPC107258
0.6133 Remote Similarity NPC476046
0.6133 Remote Similarity NPC211641
0.6133 Remote Similarity NPC251970
0.6133 Remote Similarity NPC241854
0.6133 Remote Similarity NPC471797
0.6133 Remote Similarity NPC100334
0.6133 Remote Similarity NPC128346
0.6133 Remote Similarity NPC219232
0.6125 Remote Similarity NPC472312
0.6125 Remote Similarity NPC215474
0.6125 Remote Similarity NPC283277
0.6119 Remote Similarity NPC472304
0.6119 Remote Similarity NPC276764
0.6111 Remote Similarity NPC476945
0.6111 Remote Similarity NPC160209
0.6111 Remote Similarity NPC208999
0.6111 Remote Similarity NPC87141
0.6094 Remote Similarity NPC5626
0.6087 Remote Similarity NPC283247
0.6081 Remote Similarity NPC225467
0.6081 Remote Similarity NPC234707
0.6081 Remote Similarity NPC242001
0.6071 Remote Similarity NPC183670
0.6056 Remote Similarity NPC149680
0.6056 Remote Similarity NPC185587
0.6053 Remote Similarity NPC192540
0.6053 Remote Similarity NPC28657
0.6053 Remote Similarity NPC473171
0.6053 Remote Similarity NPC257347
0.6053 Remote Similarity NPC134847
0.6053 Remote Similarity NPC162742
0.6053 Remote Similarity NPC141071
0.6053 Remote Similarity NPC285893
0.6053 Remote Similarity NPC279666
0.6053 Remote Similarity NPC288035
0.6053 Remote Similarity NPC471723
0.6053 Remote Similarity NPC230301
0.6053 Remote Similarity NPC22105
0.6053 Remote Similarity NPC136188
0.6053 Remote Similarity NPC304309
0.6053 Remote Similarity NPC293803
0.6049 Remote Similarity NPC21667
0.6049 Remote Similarity NPC171639
0.6027 Remote Similarity NPC476431
0.6 Remote Similarity NPC470045
0.6 Remote Similarity NPC470044
0.6 Remote Similarity NPC239039
0.6 Remote Similarity NPC476682
0.6 Remote Similarity NPC474122
0.6 Remote Similarity NPC474743
0.5974 Remote Similarity NPC321381

  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 NPC474528 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
0.7101 Intermediate Similarity NPD6939 Phase 2
0.7101 Intermediate Similarity NPD6938 Clinical (unspecified phase)
0.7037 Intermediate Similarity NPD1799 Clinical (unspecified phase)
0.6842 Remote Similarity NPD8028 Phase 2
0.661 Remote Similarity NPD8262 Approved
0.6571 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6479 Remote Similarity NPD4137 Phase 3
0.6415 Remote Similarity NPD319 Phase 1
0.6389 Remote Similarity NPD4691 Approved
0.6389 Remote Similarity NPD4747 Approved
0.6301 Remote Similarity NPD4243 Approved
0.6133 Remote Similarity NPD4058 Approved
0.6133 Remote Similarity NPD4784 Approved
0.6133 Remote Similarity NPD4785 Approved
0.6053 Remote Similarity NPD6942 Approved
0.6053 Remote Similarity NPD5275 Approved
0.6053 Remote Similarity NPD7339 Approved
0.6053 Remote Similarity NPD4190 Phase 3
0.5974 Remote Similarity NPD3701 Clinical (unspecified phase)
0.593 Remote Similarity NPD4096 Approved
0.5921 Remote Similarity NPD5733 Approved
0.5921 Remote Similarity NPD4687 Approved
0.5867 Remote Similarity NPD5276 Approved
0.5854 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5778 Remote Similarity NPD7732 Phase 3
0.5778 Remote Similarity NPD7614 Phase 1
0.575 Remote Similarity NPD7645 Phase 2
0.575 Remote Similarity NPD4195 Approved
0.5735 Remote Similarity NPD287 Approved
0.5698 Remote Similarity NPD4722 Approved
0.5698 Remote Similarity NPD4723 Approved
0.5672 Remote Similarity NPD4219 Approved
0.5658 Remote Similarity NPD5365 Phase 2
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