Structure

Physi-Chem Properties

Molecular Weight:  1152.68
Volume:  1178.438
LogP:  7.136
LogD:  3.278
LogS:  -3.51
# Rotatable Bonds:  12
TPSA:  342.87
# H-Bond Aceptor:  24
# H-Bond Donor:  6
# Rings:  1
# Heavy Atoms:  24

MedChem Properties

QED Drug-Likeness Score:  0.096
Synthetic Accessibility Score:  7.145
Fsp3:  0.789
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:  -5.428
MDCK Permeability:  0.00041274665272794664
Pgp-inhibitor:  1.0
Pgp-substrate:  0.993
Human Intestinal Absorption (HIA):  0.035
20% Bioavailability (F20%):  0.805
30% Bioavailability (F30%):  0.62

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.039
Plasma Protein Binding (PPB):  81.01663208007812%
Volume Distribution (VD):  0.92
Pgp-substrate:  4.44162130355835%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.0
CYP2C19-inhibitor:  0.015
CYP2C19-substrate:  0.052
CYP2C9-inhibitor:  0.007
CYP2C9-substrate:  0.003
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.014
CYP3A4-inhibitor:  0.093
CYP3A4-substrate:  0.185

ADMET: Excretion

Clearance (CL):  3.248
Half-life (T1/2):  0.148

ADMET: Toxicity

hERG Blockers:  0.001
Human Hepatotoxicity (H-HT):  1.0
Drug-inuced Liver Injury (DILI):  0.984
AMES Toxicity:  0.003
Rat Oral Acute Toxicity:  0.0
Maximum Recommended Daily Dose:  0.005
Skin Sensitization:  0.026
Carcinogencity:  0.027
Eye Corrosion:  0.418
Eye Irritation:  0.096
Respiratory Toxicity:  0.284

Download Data

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

  Natural Product: NPC138409

Natural Product ID:  NPC138409
Common Name*:   8-Isocyanatocycloamphilect-10-Ene
IUPAC Name:   (1S,3aR,4S,5aS,10aS,10bS,10cS)-10a-isocyanato-1,4,7,7-tetramethyl-1,2,3,3a,4,5,5a,6,8,10,10b,10c-dodecahydropyrene
Synonyms:  
Standard InCHIKey:  GMEIHKNXOPDFBM-OXPIXLAOSA-N
Standard InCHI:  InChI=1S/C21H31NO/c1-13-9-16-11-20(3,4)10-15-7-8-21(22-12-23)14(2)5-6-17(13)19(21)18(15)16/h7,13-14,16-19H,5-6,8-11H2,1-4H3/t13-,14-,16-,17+,18-,19-,21-/m0/s1
SMILES:  C[C@H]1C[C@H]2CC(C)(C)CC3=CC[C@@]4([C@@H](C)CC[C@H]1[C@H]4[C@H]23)N=C=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL513580
PubChem CID:   11449826
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004707] Organic nitrogen compounds
      • [CHEMONTID:0000278] Organonitrogen compounds
        • [CHEMONTID:0000501] Isocyanates

*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 = 38300.0 nM PMID[533337]

☑ 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 NPC138409 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
0.9104 High Similarity NPC184919
0.8873 High Similarity NPC476308
0.8462 Intermediate Similarity NPC317778
0.831 Intermediate Similarity NPC476329
0.8209 Intermediate Similarity NPC145715
0.8088 Intermediate Similarity NPC473959
0.791 Intermediate Similarity NPC311809
0.7846 Intermediate Similarity NPC318036
0.7761 Intermediate Similarity NPC152211
0.7761 Intermediate Similarity NPC28755
0.7746 Intermediate Similarity NPC476135
0.7727 Intermediate Similarity NPC470369
0.7727 Intermediate Similarity NPC470370
0.7612 Intermediate Similarity NPC324944
0.7571 Intermediate Similarity NPC476682
0.75 Intermediate Similarity NPC474454
0.75 Intermediate Similarity NPC474455
0.75 Intermediate Similarity NPC474420
0.7463 Intermediate Similarity NPC173815
0.7361 Intermediate Similarity NPC37792
0.7286 Intermediate Similarity NPC219621
0.725 Intermediate Similarity NPC250632
0.7206 Intermediate Similarity NPC475696
0.7206 Intermediate Similarity NPC474528
0.7206 Intermediate Similarity NPC474415
0.7206 Intermediate Similarity NPC474457
0.7183 Intermediate Similarity NPC474435
0.7183 Intermediate Similarity NPC474027
0.7164 Intermediate Similarity NPC469770
0.7143 Intermediate Similarity NPC476904
0.7123 Intermediate Similarity NPC474456
0.7105 Intermediate Similarity NPC21773
0.7067 Intermediate Similarity NPC472831
0.7 Intermediate Similarity NPC475716
0.7 Intermediate Similarity NPC472827
0.6941 Remote Similarity NPC474458
0.6883 Remote Similarity NPC265789
0.6867 Remote Similarity NPC215474
0.6824 Remote Similarity NPC152684
0.6778 Remote Similarity NPC477290
0.6769 Remote Similarity NPC22765
0.6769 Remote Similarity NPC17518
0.675 Remote Similarity NPC7214
0.6747 Remote Similarity NPC475724
0.6744 Remote Similarity NPC157479
0.6711 Remote Similarity NPC82477
0.6711 Remote Similarity NPC142754
0.6711 Remote Similarity NPC296697
0.6711 Remote Similarity NPC39157
0.6707 Remote Similarity NPC211322
0.6705 Remote Similarity NPC249312
0.6667 Remote Similarity NPC283277
0.6628 Remote Similarity NPC182106
0.6628 Remote Similarity NPC147513
0.6628 Remote Similarity NPC311769
0.6627 Remote Similarity NPC12035
0.6625 Remote Similarity NPC125828
0.6623 Remote Similarity NPC286814
0.6622 Remote Similarity NPC469662
0.6618 Remote Similarity NPC474416
0.6591 Remote Similarity NPC259252
0.6588 Remote Similarity NPC171639
0.6588 Remote Similarity NPC21667
0.6585 Remote Similarity NPC79704
0.6579 Remote Similarity NPC20181
0.6579 Remote Similarity NPC220210
0.6562 Remote Similarity NPC86683
0.6552 Remote Similarity NPC166458
0.6548 Remote Similarity NPC329782
0.6494 Remote Similarity NPC476288
0.6486 Remote Similarity NPC475755
0.6486 Remote Similarity NPC197238
0.6486 Remote Similarity NPC202118
0.6486 Remote Similarity NPC89921
0.6471 Remote Similarity NPC212905
0.6471 Remote Similarity NPC472312
0.6456 Remote Similarity NPC190035
0.6447 Remote Similarity NPC92327
0.6437 Remote Similarity NPC24733
0.6389 Remote Similarity NPC60772
0.6375 Remote Similarity NPC474488
0.6364 Remote Similarity NPC124851
0.6364 Remote Similarity NPC176107
0.6353 Remote Similarity NPC118329
0.6353 Remote Similarity NPC152039
0.6353 Remote Similarity NPC257962
0.6316 Remote Similarity NPC140685
0.6304 Remote Similarity NPC476752
0.6304 Remote Similarity NPC476753
0.6296 Remote Similarity NPC211641
0.6282 Remote Similarity NPC20610
0.6267 Remote Similarity NPC474086
0.625 Remote Similarity NPC225467
0.625 Remote Similarity NPC75810
0.625 Remote Similarity NPC192529
0.6237 Remote Similarity NPC243985
0.6237 Remote Similarity NPC280710
0.6237 Remote Similarity NPC476754
0.6234 Remote Similarity NPC286669
0.6234 Remote Similarity NPC323005
0.6234 Remote Similarity NPC222366
0.6234 Remote Similarity NPC476039
0.622 Remote Similarity NPC293803
0.6211 Remote Similarity NPC167419
0.6203 Remote Similarity NPC182815
0.6203 Remote Similarity NPC139397
0.6197 Remote Similarity NPC123194
0.6176 Remote Similarity NPC476681
0.6164 Remote Similarity NPC469769
0.6163 Remote Similarity NPC90150
0.6154 Remote Similarity NPC197805
0.6154 Remote Similarity NPC202189
0.6154 Remote Similarity NPC193770
0.6145 Remote Similarity NPC112680
0.6143 Remote Similarity NPC127944
0.6136 Remote Similarity NPC477289
0.6133 Remote Similarity NPC469728
0.6125 Remote Similarity NPC265782
0.6125 Remote Similarity NPC307176
0.6125 Remote Similarity NPC477856
0.6125 Remote Similarity NPC159577
0.6125 Remote Similarity NPC2634
0.6125 Remote Similarity NPC260040
0.6125 Remote Similarity NPC214770
0.6125 Remote Similarity NPC251929
0.6125 Remote Similarity NPC35734
0.6125 Remote Similarity NPC282593
0.6098 Remote Similarity NPC219232
0.6098 Remote Similarity NPC128346
0.6098 Remote Similarity NPC100334
0.6094 Remote Similarity NPC193180
0.6092 Remote Similarity NPC224072
0.6087 Remote Similarity NPC474964
0.6087 Remote Similarity NPC477288
0.6076 Remote Similarity NPC260474
0.6076 Remote Similarity NPC188292
0.6076 Remote Similarity NPC310992
0.6076 Remote Similarity NPC94192
0.6071 Remote Similarity NPC471897
0.6071 Remote Similarity NPC471899
0.6071 Remote Similarity NPC107039
0.6061 Remote Similarity NPC296337
0.6061 Remote Similarity NPC114239
0.6061 Remote Similarity NPC13991
0.6061 Remote Similarity NPC241784
0.6053 Remote Similarity NPC477740
0.6049 Remote Similarity NPC54123
0.6049 Remote Similarity NPC115023
0.6049 Remote Similarity NPC470078
0.6042 Remote Similarity NPC240650
0.6026 Remote Similarity NPC242945
0.6026 Remote Similarity NPC176171
0.6026 Remote Similarity NPC259156
0.6023 Remote Similarity NPC477584
0.6022 Remote Similarity NPC476064
0.6 Remote Similarity NPC115515
0.6 Remote Similarity NPC280654
0.6 Remote Similarity NPC56107
0.6 Remote Similarity NPC110094
0.6 Remote Similarity NPC127582
0.6 Remote Similarity NPC260385
0.5977 Remote Similarity NPC474122
0.5976 Remote Similarity NPC303613
0.5976 Remote Similarity NPC474228
0.5976 Remote Similarity NPC251705
0.5974 Remote Similarity NPC52449
0.5974 Remote Similarity NPC285371
0.5974 Remote Similarity NPC475124
0.5974 Remote Similarity NPC169275
0.596 Remote Similarity NPC152718
0.596 Remote Similarity NPC58200
0.596 Remote Similarity NPC226509
0.5957 Remote Similarity NPC93027
0.5952 Remote Similarity NPC290598
0.5952 Remote Similarity NPC106364
0.5952 Remote Similarity NPC265328
0.5952 Remote Similarity NPC292589
0.5952 Remote Similarity NPC89294
0.5952 Remote Similarity NPC30590
0.5952 Remote Similarity NPC27765
0.5952 Remote Similarity NPC120098
0.5952 Remote Similarity NPC122418
0.5946 Remote Similarity NPC472830
0.5938 Remote Similarity NPC103290
0.5938 Remote Similarity NPC247220
0.5938 Remote Similarity NPC476903
0.5934 Remote Similarity NPC43308
0.593 Remote Similarity NPC199595
0.593 Remote Similarity NPC16394
0.593 Remote Similarity NPC231431
0.5926 Remote Similarity NPC475728
0.5926 Remote Similarity NPC40574
0.5921 Remote Similarity NPC477739
0.5921 Remote Similarity NPC60565
0.5918 Remote Similarity NPC275686
0.5915 Remote Similarity NPC476679
0.5914 Remote Similarity NPC84171
0.5909 Remote Similarity NPC39966
0.5909 Remote Similarity NPC248411
0.5909 Remote Similarity NPC477583

  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 NPC138409 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
0.6753 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6753 Remote Similarity NPD6939 Phase 2
0.6495 Remote Similarity NPD7812 Clinical (unspecified phase)
0.6282 Remote Similarity NPD3621 Clinical (unspecified phase)
0.625 Remote Similarity NPD5365 Phase 2
0.6237 Remote Similarity NPD5769 Clinical (unspecified phase)
0.6237 Remote Similarity NPD5771 Approved
0.6203 Remote Similarity NPD4137 Phase 3
0.6163 Remote Similarity NPD8028 Phase 2
0.6125 Remote Similarity NPD4691 Approved
0.6125 Remote Similarity NPD4747 Approved
0.5904 Remote Similarity NPD4058 Approved
0.5854 Remote Similarity NPD4243 Approved
0.5846 Remote Similarity NPD1799 Clinical (unspecified phase)
0.5843 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5773 Remote Similarity NPD2895 Discontinued
0.5747 Remote Similarity NPD7645 Phase 2
0.5714 Remote Similarity NPD4785 Approved
0.5714 Remote Similarity NPD5733 Approved
0.5714 Remote Similarity NPD4784 Approved
0.5714 Remote Similarity NPD4687 Approved
0.5699 Remote Similarity NPD4722 Approved
0.5699 Remote Similarity NPD4723 Approved
0.5672 Remote Similarity NPD871 Approved
0.5672 Remote Similarity NPD873 Approved
0.5663 Remote Similarity NPD5276 Approved
0.5647 Remote Similarity NPD4190 Phase 3
0.5647 Remote Similarity NPD6942 Approved
0.5647 Remote Similarity NPD5275 Approved
0.5647 Remote Similarity NPD7339 Approved
0.561 Remote Similarity NPD15 Approved
0.561 Remote Similarity NPD791 Approved
0.56 Remote Similarity NPD6404 Discontinued

  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