Structure

Physi-Chem Properties

Molecular Weight:  263.17
Volume:  289.776
LogP:  5.88
LogD:  4.308
LogS:  -5.675
# Rotatable Bonds:  2
TPSA:  12.36
# H-Bond Aceptor:  1
# H-Bond Donor:  0
# Rings:  2
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.386
Synthetic Accessibility Score:  4.629
Fsp3:  0.812
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.589
MDCK Permeability:  1.7238322470802814e-05
Pgp-inhibitor:  0.313
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.43
30% Bioavailability (F30%):  0.453

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.948
Plasma Protein Binding (PPB):  65.45830535888672%
Volume Distribution (VD):  1.526
Pgp-substrate:  15.644858360290527%

ADMET: Metabolism

CYP1A2-inhibitor:  0.087
CYP1A2-substrate:  0.432
CYP2C19-inhibitor:  0.052
CYP2C19-substrate:  0.922
CYP2C9-inhibitor:  0.028
CYP2C9-substrate:  0.139
CYP2D6-inhibitor:  0.9
CYP2D6-substrate:  0.465
CYP3A4-inhibitor:  0.882
CYP3A4-substrate:  0.552

ADMET: Excretion

Clearance (CL):  3.371
Half-life (T1/2):  0.057

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.099
Drug-inuced Liver Injury (DILI):  0.209
AMES Toxicity:  0.011
Rat Oral Acute Toxicity:  0.86
Maximum Recommended Daily Dose:  0.929
Skin Sensitization:  0.318
Carcinogencity:  0.591
Eye Corrosion:  0.801
Eye Irritation:  0.826
Respiratory Toxicity:  0.977

Download Data

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

  Natural Product: NPC311809

Natural Product ID:  NPC311809
Common Name*:   (1S,4Ar,7S)-7-(2-Isothiocyanatopropan-2-Yl)-1,4A-Dimethyl-2,3,4,5,6,7-Hexahydro-1H-Naphthalene
IUPAC Name:   (1S,4aR,7S)-7-(2-isothiocyanatopropan-2-yl)-1,4a-dimethyl-2,3,4,5,6,7-hexahydro-1H-naphthalene
Synonyms:  
Standard InCHIKey:  YZYZKKAHYRXPMB-HEHGZKQESA-N
Standard InCHI:  InChI=1S/C16H25NS/c1-12-6-5-8-16(4)9-7-13(10-14(12)16)15(2,3)17-11-18/h10,12-13H,5-9H2,1-4H3/t12-,13-,16+/m0/s1
SMILES:  C[C@H]1CCC[C@]2(C)CC[C@@H](C=C12)C(C)(C)N=C=S
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL509424
PubChem CID:   9992945
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0000101] Eudesmane, isoeudesmane or cycloeudesmane sesquiterpenoids

*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
NPO4958 Acanthella klethra Species Melastomataceae Eukaryota n.a. n.a. n.a. PMID[1294700]
NPO4958 Acanthella klethra Species Melastomataceae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ 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 > 20.0 ug.mL-1 PMID[447470]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 2.24 ug.mL-1 PMID[447470]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 0.61 ug.mL-1 PMID[447470]

☑ 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 NPC311809 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
0.9 High Similarity NPC145715
0.8852 High Similarity NPC473959
0.875 High Similarity NPC184919
0.85 High Similarity NPC28755
0.85 High Similarity NPC152211
0.8281 Intermediate Similarity NPC37792
0.791 Intermediate Similarity NPC138409
0.7869 Intermediate Similarity NPC470369
0.7869 Intermediate Similarity NPC470370
0.7727 Intermediate Similarity NPC474456
0.75 Intermediate Similarity NPC317778
0.75 Intermediate Similarity NPC86683
0.7414 Intermediate Similarity NPC17518
0.7385 Intermediate Similarity NPC219621
0.7344 Intermediate Similarity NPC472827
0.7302 Intermediate Similarity NPC474528
0.7302 Intermediate Similarity NPC475696
0.7302 Intermediate Similarity NPC474415
0.726 Intermediate Similarity NPC476308
0.7164 Intermediate Similarity NPC476682
0.7119 Intermediate Similarity NPC22765
0.7105 Intermediate Similarity NPC250632
0.7077 Intermediate Similarity NPC474454
0.7077 Intermediate Similarity NPC474455
0.7077 Intermediate Similarity NPC475716
0.7077 Intermediate Similarity NPC474420
0.7031 Intermediate Similarity NPC474457
0.7013 Intermediate Similarity NPC475724
0.6949 Remote Similarity NPC124851
0.6944 Remote Similarity NPC476329
0.6944 Remote Similarity NPC21773
0.6944 Remote Similarity NPC265789
0.6901 Remote Similarity NPC472831
0.6875 Remote Similarity NPC318036
0.6842 Remote Similarity NPC192529
0.6774 Remote Similarity NPC473728
0.6769 Remote Similarity NPC173815
0.6757 Remote Similarity NPC476904
0.6724 Remote Similarity NPC202189
0.6721 Remote Similarity NPC476681
0.6721 Remote Similarity NPC472829
0.6719 Remote Similarity NPC469770
0.6667 Remote Similarity NPC475272
0.6667 Remote Similarity NPC324944
0.6667 Remote Similarity NPC472830
0.6667 Remote Similarity NPC125828
0.6623 Remote Similarity NPC79704
0.661 Remote Similarity NPC13991
0.661 Remote Similarity NPC296337
0.661 Remote Similarity NPC241784
0.661 Remote Similarity NPC114239
0.6579 Remote Similarity NPC7214
0.6562 Remote Similarity NPC476683
0.6557 Remote Similarity NPC106990
0.6522 Remote Similarity NPC474086
0.65 Remote Similarity NPC283277
0.6491 Remote Similarity NPC103290
0.6462 Remote Similarity NPC123194
0.6441 Remote Similarity NPC248411
0.6418 Remote Similarity NPC469769
0.6406 Remote Similarity NPC476679
0.6406 Remote Similarity NPC474416
0.6389 Remote Similarity NPC476135
0.6386 Remote Similarity NPC474458
0.6379 Remote Similarity NPC105246
0.6379 Remote Similarity NPC190232
0.6379 Remote Similarity NPC193180
0.6296 Remote Similarity NPC224072
0.629 Remote Similarity NPC17810
0.6286 Remote Similarity NPC472544
0.6286 Remote Similarity NPC474596
0.6265 Remote Similarity NPC24733
0.625 Remote Similarity NPC12035
0.6212 Remote Similarity NPC470893
0.619 Remote Similarity NPC166458
0.619 Remote Similarity NPC200129
0.6176 Remote Similarity NPC60772
0.6173 Remote Similarity NPC118329
0.6173 Remote Similarity NPC329782
0.6173 Remote Similarity NPC152039
0.6173 Remote Similarity NPC474122
0.6143 Remote Similarity NPC469728
0.6133 Remote Similarity NPC472543
0.6125 Remote Similarity NPC211322
0.6102 Remote Similarity NPC177470
0.6098 Remote Similarity NPC39966
0.6098 Remote Similarity NPC472312
0.6098 Remote Similarity NPC215474
0.6066 Remote Similarity NPC49088
0.6056 Remote Similarity NPC202118
0.6056 Remote Similarity NPC475755
0.6056 Remote Similarity NPC197238
0.6034 Remote Similarity NPC227632
0.6034 Remote Similarity NPC78551
0.6034 Remote Similarity NPC62086
0.6029 Remote Similarity NPC11130
0.6024 Remote Similarity NPC171639
0.6 Remote Similarity NPC60556
0.6 Remote Similarity NPC86538
0.6 Remote Similarity NPC109813
0.6 Remote Similarity NPC127582
0.5977 Remote Similarity NPC249312
0.5972 Remote Similarity NPC469662
0.5968 Remote Similarity NPC323445
0.5965 Remote Similarity NPC139717
0.5965 Remote Similarity NPC297643
0.5965 Remote Similarity NPC229262
0.5942 Remote Similarity NPC231129
0.5932 Remote Similarity NPC144023
0.5904 Remote Similarity NPC471868
0.589 Remote Similarity NPC475812
0.5889 Remote Similarity NPC477290
0.5882 Remote Similarity NPC152684
0.5882 Remote Similarity NPC75810
0.5857 Remote Similarity NPC82919
0.5833 Remote Similarity NPC21667
0.5833 Remote Similarity NPC477584
0.5811 Remote Similarity NPC476039
0.5811 Remote Similarity NPC279434
0.5811 Remote Similarity NPC286669
0.5811 Remote Similarity NPC222366
0.5811 Remote Similarity NPC176171
0.5811 Remote Similarity NPC259156
0.5811 Remote Similarity NPC92327
0.5811 Remote Similarity NPC242945
0.5789 Remote Similarity NPC190810
0.5789 Remote Similarity NPC34764
0.5789 Remote Similarity NPC76145
0.5775 Remote Similarity NPC176621
0.5763 Remote Similarity NPC183670
0.5753 Remote Similarity NPC52449
0.5753 Remote Similarity NPC476559
0.5753 Remote Similarity NPC285371
0.5753 Remote Similarity NPC475124
0.5753 Remote Similarity NPC169275
0.5733 Remote Similarity NPC193770
0.5733 Remote Similarity NPC197805
0.5733 Remote Similarity NPC176107
0.5714 Remote Similarity NPC477583
0.5714 Remote Similarity NPC243985
0.5714 Remote Similarity NPC280710
0.5694 Remote Similarity NPC60565
0.569 Remote Similarity NPC239039
0.5682 Remote Similarity NPC34754
0.5676 Remote Similarity NPC268039
0.5676 Remote Similarity NPC107258
0.5676 Remote Similarity NPC163678
0.5672 Remote Similarity NPC127944
0.5672 Remote Similarity NPC14002
0.5672 Remote Similarity NPC23117
0.5658 Remote Similarity NPC142754
0.5658 Remote Similarity NPC20610
0.5658 Remote Similarity NPC476945
0.5658 Remote Similarity NPC296697
0.5658 Remote Similarity NPC188292
0.5658 Remote Similarity NPC39157
0.5658 Remote Similarity NPC260474
0.5658 Remote Similarity NPC216460
0.5658 Remote Similarity NPC208999
0.5658 Remote Similarity NPC155198
0.5658 Remote Similarity NPC310992
0.5658 Remote Similarity NPC82477
0.5647 Remote Similarity NPC161344
0.5634 Remote Similarity NPC309825
0.5634 Remote Similarity NPC276764
0.5634 Remote Similarity NPC472304
0.5632 Remote Similarity NPC157479
0.5616 Remote Similarity NPC283247
0.5616 Remote Similarity NPC81615
0.5614 Remote Similarity NPC92224
0.56 Remote Similarity NPC323005
0.56 Remote Similarity NPC149680
0.56 Remote Similarity NPC185587

  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 NPC311809 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
0.6575 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6575 Remote Similarity NPD6939 Phase 2
0.6379 Remote Similarity NPD1799 Clinical (unspecified phase)
0.629 Remote Similarity NPD8262 Approved
0.5844 Remote Similarity NPD5365 Phase 2
0.5789 Remote Similarity NPD319 Phase 1
0.5658 Remote Similarity NPD3621 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