Structure

Physi-Chem Properties

Molecular Weight:  297.27
Volume:  331.348
LogP:  3.939
LogD:  4.098
LogS:  -3.729
# Rotatable Bonds:  7
TPSA:  52.49
# H-Bond Aceptor:  3
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.632
Synthetic Accessibility Score:  4.282
Fsp3:  1.0
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.01
MDCK Permeability:  2.758181290118955e-05
Pgp-inhibitor:  0.003
Pgp-substrate:  0.994
Human Intestinal Absorption (HIA):  0.523
20% Bioavailability (F20%):  0.939
30% Bioavailability (F30%):  0.427

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.084
Plasma Protein Binding (PPB):  62.885032653808594%
Volume Distribution (VD):  1.187
Pgp-substrate:  25.394329071044922%

ADMET: Metabolism

CYP1A2-inhibitor:  0.095
CYP1A2-substrate:  0.805
CYP2C19-inhibitor:  0.124
CYP2C19-substrate:  0.633
CYP2C9-inhibitor:  0.031
CYP2C9-substrate:  0.108
CYP2D6-inhibitor:  0.196
CYP2D6-substrate:  0.834
CYP3A4-inhibitor:  0.043
CYP3A4-substrate:  0.209

ADMET: Excretion

Clearance (CL):  9.336
Half-life (T1/2):  0.311

ADMET: Toxicity

hERG Blockers:  0.139
Human Hepatotoxicity (H-HT):  0.259
Drug-inuced Liver Injury (DILI):  0.046
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.009
Maximum Recommended Daily Dose:  0.598
Skin Sensitization:  0.939
Carcinogencity:  0.037
Eye Corrosion:  0.481
Eye Irritation:  0.116
Respiratory Toxicity:  0.901

Download Data

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

  Natural Product: NPC477002

Natural Product ID:  NPC477002
Common Name*:   (2R,3S,4aR,5R,8aS)-5-(5-hydroxyoctyl)-2-methyl-1,2,3,4,4a,5,6,7,8,8a-decahydroquinolin-3-ol
IUPAC Name:   (2R,3S,4aR,5R,8aS)-5-(5-hydroxyoctyl)-2-methyl-1,2,3,4,4a,5,6,7,8,8a-decahydroquinolin-3-ol
Synonyms:  
Standard InCHIKey:  LNSIIDDYOVTXHK-WVDLQDBSSA-N
Standard InCHI:  InChI=1S/C18H35NO2/c1-3-7-15(20)10-5-4-8-14-9-6-11-17-16(14)12-18(21)13(2)19-17/h13-21H,3-12H2,1-2H3/t13-,14-,15?,16-,17+,18+/m1/s1
SMILES:  CCCC(CCCC[C@@H]1CCC[C@H]2[C@@H]1C[C@@H]([C@H](N2)C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11066430
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0003787] Quinolidines

*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
NPO33591 Didemnum sp. Species Didemnidae Eukaryota n.a. Stanley Reef, the Great Barrier Reef, Queensland, Australia 1983-MAY PMID[12086492]
NPO33591 Didemnum sp. Species Didemnidae Eukaryota n.a. n.a. n.a. PMID[19299148]
NPO33591 Didemnum sp. Species Didemnidae Eukaryota n.a. Tiwai Wharf, Tiwai Point, Southland, New Zealand (4635.52' S, 16821.14' E) 2007-AUG PMID[21348447]
NPO33591 Didemnum sp. Species Didemnidae Eukaryota n.a. at a depth of 7 m from wooden piles at Tiwai Wharf, Tiwai Point, Southland, New Zealand (4635.52' S, 16821.14' E) 2007-AUG PMID[21348447]

☑ 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
NPT839 Cell Line L6 Rattus norvegicus IC50 > 30 ug/ml PMID[12086492]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 6.1 ug/ml PMID[12086492]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 10 ug/ml PMID[12086492]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi IC50 = 37.2 ug/ml PMID[12086492]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense IC50 = 5.6 ug/ml PMID[12086492]
NPT1231 Organism Microbotryum violaceum Microbotryum violaceum IZ = 2 mm PMID[12086492]
NPT1232 Organism Eurotium repens Eurotium repens IZ = 1 mm PMID[12086492]
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 = 4 ug/ml PMID[12086492]
NPT580 Organism Trypanosoma cruzi Trypanosoma cruzi IC50 = 37.3 ug/ml PMID[12086492]
NPT844 Organism Trypanosoma brucei rhodesiense Trypanosoma brucei rhodesiense IC50 = 1.97 ug/ml PMID[12086492]

☑ 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 NPC477002 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
0.7403 Intermediate Similarity NPC476694
0.7403 Intermediate Similarity NPC476696
0.7403 Intermediate Similarity NPC306973
0.7403 Intermediate Similarity NPC476695
0.7188 Intermediate Similarity NPC477001
0.7188 Intermediate Similarity NPC477000
0.7143 Intermediate Similarity NPC268922
0.7045 Intermediate Similarity NPC21035
0.7013 Intermediate Similarity NPC471418
0.6882 Remote Similarity NPC25033
0.6882 Remote Similarity NPC119225
0.6882 Remote Similarity NPC174117
0.6882 Remote Similarity NPC155985
0.6882 Remote Similarity NPC470382
0.6882 Remote Similarity NPC471635
0.6882 Remote Similarity NPC476261
0.6753 Remote Similarity NPC303798
0.6753 Remote Similarity NPC286851
0.6714 Remote Similarity NPC123814
0.6714 Remote Similarity NPC474322
0.6712 Remote Similarity NPC204709
0.6667 Remote Similarity NPC112398
0.6633 Remote Similarity NPC176012
0.6623 Remote Similarity NPC223386
0.6623 Remote Similarity NPC471780
0.6623 Remote Similarity NPC142290
0.6623 Remote Similarity NPC471892
0.6623 Remote Similarity NPC198341
0.6623 Remote Similarity NPC75435
0.6622 Remote Similarity NPC471421
0.6622 Remote Similarity NPC290106
0.6622 Remote Similarity NPC76726
0.6622 Remote Similarity NPC193593
0.6622 Remote Similarity NPC143809
0.6622 Remote Similarity NPC233364
0.6562 Remote Similarity NPC473537
0.6562 Remote Similarity NPC474164
0.6512 Remote Similarity NPC90839
0.6495 Remote Similarity NPC475249
0.6495 Remote Similarity NPC252564
0.6458 Remote Similarity NPC289140
0.6429 Remote Similarity NPC201712
0.6386 Remote Similarity NPC208657
0.6377 Remote Similarity NPC96966
0.6377 Remote Similarity NPC29222
0.6377 Remote Similarity NPC121062
0.6364 Remote Similarity NPC306462
0.6364 Remote Similarity NPC22774
0.6364 Remote Similarity NPC218150
0.6364 Remote Similarity NPC150680
0.6364 Remote Similarity NPC475518
0.6364 Remote Similarity NPC2432
0.6364 Remote Similarity NPC69669
0.6364 Remote Similarity NPC109533
0.6351 Remote Similarity NPC8979
0.6327 Remote Similarity NPC220111
0.6292 Remote Similarity NPC93630
0.6282 Remote Similarity NPC163134
0.6282 Remote Similarity NPC471419
0.6277 Remote Similarity NPC312637
0.6265 Remote Similarity NPC474468
0.622 Remote Similarity NPC475694
0.622 Remote Similarity NPC473710
0.6207 Remote Similarity NPC473972
0.6207 Remote Similarity NPC475363
0.6207 Remote Similarity NPC473971
0.6204 Remote Similarity NPC28280
0.6204 Remote Similarity NPC304646
0.62 Remote Similarity NPC118275
0.619 Remote Similarity NPC26932
0.618 Remote Similarity NPC45906
0.618 Remote Similarity NPC149908
0.618 Remote Similarity NPC288415
0.618 Remote Similarity NPC31313
0.617 Remote Similarity NPC323156
0.6145 Remote Similarity NPC28959
0.6145 Remote Similarity NPC285014
0.6145 Remote Similarity NPC299603
0.6145 Remote Similarity NPC255535
0.6145 Remote Similarity NPC137554
0.6129 Remote Similarity NPC470282
0.6125 Remote Similarity NPC315980
0.6104 Remote Similarity NPC319131
0.6095 Remote Similarity NPC253645
0.6095 Remote Similarity NPC95920
0.6095 Remote Similarity NPC85001
0.6095 Remote Similarity NPC147835
0.6061 Remote Similarity NPC292819
0.6055 Remote Similarity NPC476955
0.6023 Remote Similarity NPC39308
0.6019 Remote Similarity NPC475239
0.6 Remote Similarity NPC81006
0.6 Remote Similarity NPC233034
0.6 Remote Similarity NPC271772
0.6 Remote Similarity NPC474928
0.6 Remote Similarity NPC36927
0.5976 Remote Similarity NPC195165
0.5957 Remote Similarity NPC168017
0.5952 Remote Similarity NPC477200
0.5949 Remote Similarity NPC17455
0.5946 Remote Similarity NPC270041
0.5946 Remote Similarity NPC277072
0.5946 Remote Similarity NPC178263
0.5943 Remote Similarity NPC473994
0.5941 Remote Similarity NPC135799
0.5921 Remote Similarity NPC471605
0.5921 Remote Similarity NPC471443
0.5905 Remote Similarity NPC244982
0.5905 Remote Similarity NPC476756
0.5877 Remote Similarity NPC478138
0.587 Remote Similarity NPC320936
0.5849 Remote Similarity NPC159367
0.5843 Remote Similarity NPC98750
0.5833 Remote Similarity NPC178632
0.5823 Remote Similarity NPC57846
0.5823 Remote Similarity NPC474014
0.5823 Remote Similarity NPC30126
0.58 Remote Similarity NPC476903
0.5784 Remote Similarity NPC56298
0.5784 Remote Similarity NPC471628
0.5783 Remote Similarity NPC126664
0.5783 Remote Similarity NPC107224
0.5783 Remote Similarity NPC34291
0.578 Remote Similarity NPC124358
0.5778 Remote Similarity NPC70574
0.5773 Remote Similarity NPC84171
0.5769 Remote Similarity NPC216415
0.5769 Remote Similarity NPC170172
0.5769 Remote Similarity NPC476537
0.5769 Remote Similarity NPC241879
0.5765 Remote Similarity NPC255050
0.5765 Remote Similarity NPC127553
0.5755 Remote Similarity NPC267217
0.5755 Remote Similarity NPC48127
0.5755 Remote Similarity NPC83047
0.5755 Remote Similarity NPC8009
0.5741 Remote Similarity NPC139778
0.5733 Remote Similarity NPC272396
0.5732 Remote Similarity NPC116377
0.5732 Remote Similarity NPC77191
0.5732 Remote Similarity NPC473952
0.5732 Remote Similarity NPC101746
0.5732 Remote Similarity NPC69798
0.5714 Remote Similarity NPC470596
0.5714 Remote Similarity NPC471420
0.57 Remote Similarity NPC311164
0.57 Remote Similarity NPC272732
0.5694 Remote Similarity NPC193872
0.5688 Remote Similarity NPC66862
0.5686 Remote Similarity NPC91604
0.5684 Remote Similarity NPC306838
0.5682 Remote Similarity NPC244539
0.5678 Remote Similarity NPC317654
0.5678 Remote Similarity NPC96010
0.5663 Remote Similarity NPC113224
0.5658 Remote Similarity NPC471442
0.5658 Remote Similarity NPC471423
0.5652 Remote Similarity NPC192456
0.5641 Remote Similarity NPC302569
0.5641 Remote Similarity NPC168308
0.5638 Remote Similarity NPC277918
0.5625 Remote Similarity NPC8087
0.5625 Remote Similarity NPC314510
0.5625 Remote Similarity NPC62507
0.5618 Remote Similarity NPC25110
0.5614 Remote Similarity NPC475340
0.561 Remote Similarity NPC41429
0.5607 Remote Similarity NPC317534
0.5607 Remote Similarity NPC46981

  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 NPC477002 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
0.6714 Remote Similarity NPD3215 Phase 1
0.6667 Remote Similarity NPD3214 Discontinued
0.6562 Remote Similarity NPD7919 Phase 3
0.6562 Remote Similarity NPD7920 Phase 3
0.6495 Remote Similarity NPD8088 Phase 1
0.6479 Remote Similarity NPD3721 Approved
0.6479 Remote Similarity NPD3722 Approved
0.6447 Remote Similarity NPD9024 Phase 2
0.6447 Remote Similarity NPD9022 Phase 2
0.6364 Remote Similarity NPD9028 Phase 2
0.6364 Remote Similarity NPD9026 Phase 2
0.6364 Remote Similarity NPD9027 Phase 3
0.6364 Remote Similarity NPD9029 Phase 3
0.6304 Remote Similarity NPD621 Discontinued
0.6264 Remote Similarity NPD394 Phase 3
0.6207 Remote Similarity NPD617 Approved
0.6071 Remote Similarity NPD3187 Discontinued
0.6042 Remote Similarity NPD6699 Clinical (unspecified phase)
0.6026 Remote Similarity NPD393 Approved
0.6022 Remote Similarity NPD8308 Discontinued
0.6 Remote Similarity NPD9440 Discontinued
0.6 Remote Similarity NPD9648 Approved
0.5962 Remote Similarity NPD6920 Discontinued
0.5926 Remote Similarity NPD7337 Clinical (unspecified phase)
0.5926 Remote Similarity NPD7336 Phase 2
0.5926 Remote Similarity NPD7335 Phase 2
0.5909 Remote Similarity NPD8144 Approved
0.5909 Remote Similarity NPD8143 Approved
0.5905 Remote Similarity NPD7646 Clinical (unspecified phase)
0.5897 Remote Similarity NPD9455 Approved
0.589 Remote Similarity NPD7348 Clinical (unspecified phase)
0.5849 Remote Similarity NPD6415 Discontinued
0.5833 Remote Similarity NPD2694 Approved
0.5833 Remote Similarity NPD2695 Approved
0.5833 Remote Similarity NPD2697 Approved
0.5833 Remote Similarity NPD2696 Approved
0.5814 Remote Similarity NPD355 Phase 2
0.5811 Remote Similarity NPD9668 Phase 2
0.5802 Remote Similarity NPD4272 Discontinued
0.5784 Remote Similarity NPD4838 Approved
0.5784 Remote Similarity NPD4835 Approved
0.5784 Remote Similarity NPD4836 Approved
0.5784 Remote Similarity NPD4837 Approved
0.5783 Remote Similarity NPD9443 Clinical (unspecified phase)
0.5743 Remote Similarity NPD3714 Approved
0.5743 Remote Similarity NPD3713 Approved
0.5743 Remote Similarity NPD3715 Approved
0.5696 Remote Similarity NPD9239 Approved
0.5696 Remote Similarity NPD9240 Approved
0.5684 Remote Similarity NPD3176 Clinical (unspecified phase)
0.5652 Remote Similarity NPD390 Approved
0.5652 Remote Similarity NPD718 Approved
0.5612 Remote Similarity NPD2682 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