Structure

Physi-Chem Properties

Molecular Weight:  297.25
Volume:  346.554
LogP:  5.633
LogD:  4.725
LogS:  -5.701
# 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:  0.592
Synthetic Accessibility Score:  5.055
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:  -4.686
MDCK Permeability:  2.0723971829283983e-05
Pgp-inhibitor:  0.985
Pgp-substrate:  0.263
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.974
30% Bioavailability (F30%):  0.814

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.647
Plasma Protein Binding (PPB):  94.00614166259766%
Volume Distribution (VD):  2.718
Pgp-substrate:  9.025718688964844%

ADMET: Metabolism

CYP1A2-inhibitor:  0.736
CYP1A2-substrate:  0.667
CYP2C19-inhibitor:  0.483
CYP2C19-substrate:  0.827
CYP2C9-inhibitor:  0.427
CYP2C9-substrate:  0.047
CYP2D6-inhibitor:  0.102
CYP2D6-substrate:  0.025
CYP3A4-inhibitor:  0.846
CYP3A4-substrate:  0.797

ADMET: Excretion

Clearance (CL):  15.022
Half-life (T1/2):  0.099

ADMET: Toxicity

hERG Blockers:  0.093
Human Hepatotoxicity (H-HT):  0.407
Drug-inuced Liver Injury (DILI):  0.91
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.809
Maximum Recommended Daily Dose:  0.952
Skin Sensitization:  0.952
Carcinogencity:  0.775
Eye Corrosion:  0.993
Eye Irritation:  0.856
Respiratory Toxicity:  0.991

Download Data

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

  Natural Product: NPC475716

Natural Product ID:  NPC475716
Common Name*:   (3S*,4R*,7S*,8S*,11S*,13S*)-8-Isocyanoamphilecta-1(12),14-Diene
IUPAC Name:   (1S,3aS,4S,6aR,7S,9bS)-1,4,7-trimethyl-9-(2-methylprop-1-enyl)-1,2,3,4,5,6,6a,7,8,9b-decahydrophenalene-3a-carbonitrile
Synonyms:  
Standard InCHIKey:  RZOWSZJNZPHIJY-XDBTUQKASA-N
Standard InCHI:  InChI=1S/C21H31N/c1-13(2)10-17-11-15(4)18-7-6-16(5)21(12-22)9-8-14(3)19(17)20(18)21/h10,14-16,18,20H,6-9,11H2,1-5H3/t14-,15-,16-,18+,20-,21-/m0/s1
SMILES:  N#C[C@@]12CC[C@@H](C3=C(C[C@@H]([C@H]([C@H]23)CC[C@@H]1C)C)C=C(C)C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL512513
PubChem CID:   44559505
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001549] Monoterpenoids

*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 = 11200.0 nM PMID[561862]

☑ 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 NPC475716 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 NPC475696
0.9636 High Similarity NPC474415
0.9636 High Similarity NPC474528
0.9298 High Similarity NPC474454
0.9298 High Similarity NPC474455
0.9298 High Similarity NPC474420
0.9286 High Similarity NPC474457
0.8833 High Similarity NPC474086
0.8571 High Similarity NPC474416
0.8571 High Similarity NPC476679
0.8364 Intermediate Similarity NPC476681
0.7857 Intermediate Similarity NPC17518
0.7857 Intermediate Similarity NPC22765
0.7667 Intermediate Similarity NPC469770
0.7636 Intermediate Similarity NPC86683
0.7581 Intermediate Similarity NPC469769
0.7368 Intermediate Similarity NPC124851
0.7344 Intermediate Similarity NPC317778
0.7273 Intermediate Similarity NPC192529
0.7188 Intermediate Similarity NPC472827
0.7143 Intermediate Similarity NPC202189
0.7097 Intermediate Similarity NPC123194
0.7097 Intermediate Similarity NPC470893
0.7091 Intermediate Similarity NPC193180
0.7077 Intermediate Similarity NPC311809
0.7059 Intermediate Similarity NPC474456
0.7018 Intermediate Similarity NPC13991
0.7018 Intermediate Similarity NPC114239
0.7018 Intermediate Similarity NPC296337
0.7018 Intermediate Similarity NPC241784
0.7 Intermediate Similarity NPC184919
0.7 Intermediate Similarity NPC138409
0.697 Remote Similarity NPC469728
0.697 Remote Similarity NPC219621
0.6949 Remote Similarity NPC17810
0.6909 Remote Similarity NPC103290
0.6875 Remote Similarity NPC470369
0.6875 Remote Similarity NPC470370
0.6842 Remote Similarity NPC248411
0.6806 Remote Similarity NPC265789
0.6806 Remote Similarity NPC21773
0.6786 Remote Similarity NPC177470
0.6786 Remote Similarity NPC190232
0.6786 Remote Similarity NPC105246
0.6765 Remote Similarity NPC469662
0.6719 Remote Similarity NPC318036
0.6714 Remote Similarity NPC193770
0.6667 Remote Similarity NPC476683
0.6625 Remote Similarity NPC477289
0.6622 Remote Similarity NPC476904
0.662 Remote Similarity NPC310992
0.662 Remote Similarity NPC32055
0.662 Remote Similarity NPC216460
0.6618 Remote Similarity NPC202118
0.6618 Remote Similarity NPC145715
0.6618 Remote Similarity NPC197238
0.6615 Remote Similarity NPC173815
0.6613 Remote Similarity NPC473728
0.6607 Remote Similarity NPC144023
0.6575 Remote Similarity NPC470078
0.6571 Remote Similarity NPC92327
0.6571 Remote Similarity NPC222366
0.6571 Remote Similarity NPC286669
0.6571 Remote Similarity NPC476039
0.6567 Remote Similarity NPC176621
0.6557 Remote Similarity NPC200129
0.6533 Remote Similarity NPC125828
0.6522 Remote Similarity NPC473959
0.6515 Remote Similarity NPC324944
0.6515 Remote Similarity NPC60772
0.6508 Remote Similarity NPC127944
0.6479 Remote Similarity NPC197805
0.6479 Remote Similarity NPC176107
0.6447 Remote Similarity NPC476308
0.6447 Remote Similarity NPC7214
0.6429 Remote Similarity NPC268039
0.6429 Remote Similarity NPC183670
0.6418 Remote Similarity NPC28755
0.6418 Remote Similarity NPC152211
0.6389 Remote Similarity NPC20610
0.6389 Remote Similarity NPC82477
0.6389 Remote Similarity NPC296697
0.6389 Remote Similarity NPC39157
0.6389 Remote Similarity NPC142754
0.6364 Remote Similarity NPC139717
0.6364 Remote Similarity NPC239039
0.6364 Remote Similarity NPC297643
0.6364 Remote Similarity NPC229262
0.6338 Remote Similarity NPC323005
0.6338 Remote Similarity NPC37792
0.6338 Remote Similarity NPC149680
0.6316 Remote Similarity NPC473171
0.6301 Remote Similarity NPC139397
0.6301 Remote Similarity NPC476431
0.6301 Remote Similarity NPC286814
0.6301 Remote Similarity NPC182815
0.625 Remote Similarity NPC220210
0.625 Remote Similarity NPC20181
0.6234 Remote Similarity NPC112680
0.6234 Remote Similarity NPC292589
0.6216 Remote Similarity NPC2634
0.6216 Remote Similarity NPC475728
0.6216 Remote Similarity NPC260040
0.6216 Remote Similarity NPC282593
0.6216 Remote Similarity NPC265782
0.6216 Remote Similarity NPC307176
0.6216 Remote Similarity NPC159577
0.6216 Remote Similarity NPC251929
0.6216 Remote Similarity NPC35734
0.6197 Remote Similarity NPC163678
0.6182 Remote Similarity NPC190810
0.6182 Remote Similarity NPC76145
0.6182 Remote Similarity NPC34764
0.6167 Remote Similarity NPC49088
0.6164 Remote Similarity NPC188292
0.6164 Remote Similarity NPC94192
0.6164 Remote Similarity NPC260474
0.614 Remote Similarity NPC227632
0.614 Remote Similarity NPC78551
0.614 Remote Similarity NPC62086
0.6133 Remote Similarity NPC54123
0.6133 Remote Similarity NPC115023
0.6133 Remote Similarity NPC190035
0.6133 Remote Similarity NPC476329
0.6125 Remote Similarity NPC12035
0.6119 Remote Similarity NPC11130
0.6111 Remote Similarity NPC279434
0.6111 Remote Similarity NPC242945
0.6111 Remote Similarity NPC176171
0.6111 Remote Similarity NPC259156
0.6104 Remote Similarity NPC471468
0.6102 Remote Similarity NPC86538
0.6102 Remote Similarity NPC109813
0.6102 Remote Similarity NPC60556
0.6087 Remote Similarity NPC127582
0.6081 Remote Similarity NPC472831
0.6076 Remote Similarity NPC76931
0.6076 Remote Similarity NPC18603
0.6076 Remote Similarity NPC307965
0.6071 Remote Similarity NPC266298
0.6071 Remote Similarity NPC45727
0.6071 Remote Similarity NPC48638
0.6066 Remote Similarity NPC323445
0.6056 Remote Similarity NPC475124
0.6056 Remote Similarity NPC285371
0.6056 Remote Similarity NPC169275
0.6056 Remote Similarity NPC52449
0.6053 Remote Similarity NPC474228
0.6053 Remote Similarity NPC471799
0.6053 Remote Similarity NPC182717
0.6053 Remote Similarity NPC474488
0.6053 Remote Similarity NPC303613
0.6053 Remote Similarity NPC251705
0.6049 Remote Similarity NPC152039
0.6049 Remote Similarity NPC118329
0.6049 Remote Similarity NPC329782
0.6034 Remote Similarity NPC120926
0.6034 Remote Similarity NPC218918
0.6029 Remote Similarity NPC472830
0.6026 Remote Similarity NPC899
0.6026 Remote Similarity NPC106432
0.6026 Remote Similarity NPC309399
0.6 Remote Similarity NPC477856
0.6 Remote Similarity NPC211322
0.6 Remote Similarity NPC214770
0.6 Remote Similarity NPC60565
0.6 Remote Similarity NPC145498
0.5976 Remote Similarity NPC215474
0.5976 Remote Similarity NPC283277
0.5976 Remote Similarity NPC472312
0.5974 Remote Similarity NPC241854
0.5974 Remote Similarity NPC211641
0.5974 Remote Similarity NPC251970
0.5974 Remote Similarity NPC329866
0.5974 Remote Similarity NPC100334
0.5974 Remote Similarity NPC474796
0.5974 Remote Similarity NPC219232
0.5974 Remote Similarity NPC474797
0.5974 Remote Similarity NPC471797
0.5974 Remote Similarity NPC476046
0.5974 Remote Similarity NPC128346
0.5972 Remote Similarity NPC107258
0.597 Remote Similarity NPC249645
0.597 Remote Similarity NPC55412
0.5949 Remote Similarity NPC249018
0.5949 Remote Similarity NPC3190
0.5946 Remote Similarity NPC160209
0.5946 Remote Similarity NPC87141
0.5946 Remote Similarity NPC476945
0.5946 Remote Similarity NPC208999
0.5942 Remote Similarity NPC472304
0.5942 Remote Similarity NPC276764
0.5921 Remote Similarity NPC225467
0.5921 Remote Similarity NPC234707
0.5921 Remote Similarity NPC242001
0.5915 Remote Similarity NPC283247
0.5909 Remote Similarity NPC5626
0.5904 Remote Similarity NPC21667
0.5904 Remote Similarity NPC171639
0.5897 Remote Similarity NPC162742

  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 NPC475716 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
0.6949 Remote Similarity NPD8262 Approved
0.6901 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6901 Remote Similarity NPD6939 Phase 2
0.6786 Remote Similarity NPD1799 Clinical (unspecified phase)
0.6667 Remote Similarity NPD8028 Phase 2
0.64 Remote Similarity NPD4058 Approved
0.6389 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6301 Remote Similarity NPD4137 Phase 3
0.6216 Remote Similarity NPD4691 Approved
0.6216 Remote Similarity NPD4747 Approved
0.6184 Remote Similarity NPD5733 Approved
0.6184 Remote Similarity NPD4687 Approved
0.6182 Remote Similarity NPD319 Phase 1
0.6163 Remote Similarity NPD4096 Approved
0.6133 Remote Similarity NPD5276 Approved
0.6133 Remote Similarity NPD4243 Approved
0.6098 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5974 Remote Similarity NPD4784 Approved
0.5974 Remote Similarity NPD4785 Approved
0.597 Remote Similarity NPD4219 Approved
0.5897 Remote Similarity NPD6942 Approved
0.5897 Remote Similarity NPD4190 Phase 3
0.5897 Remote Similarity NPD7339 Approved
0.5897 Remote Similarity NPD5275 Approved
0.5867 Remote Similarity NPD6922 Approved
0.5867 Remote Similarity NPD6923 Approved
0.5833 Remote Similarity NPD4544 Approved
0.5823 Remote Similarity NPD3701 Clinical (unspecified phase)
0.5789 Remote Similarity NPD7143 Approved
0.5789 Remote Similarity NPD7144 Approved
0.5747 Remote Similarity NPD5675 Discontinued
0.5714 Remote Similarity NPD7151 Approved
0.5714 Remote Similarity NPD7150 Approved
0.5714 Remote Similarity NPD7152 Approved
0.5652 Remote Similarity NPD7732 Phase 3
0.5652 Remote Similarity NPD7614 Phase 1
0.561 Remote Similarity NPD4195 Approved
0.561 Remote Similarity NPD7645 Phase 2

  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