Structure

Physi-Chem Properties

Molecular Weight:  315.26
Volume:  352.06
LogP:  6.16
LogD:  5.398
LogS:  -5.116
# Rotatable Bonds:  2
TPSA:  29.1
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.587
Synthetic Accessibility Score:  5.263
Fsp3:  0.857
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:  -4.65
MDCK Permeability:  4.411420377437025e-05
Pgp-inhibitor:  0.017
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.323
30% Bioavailability (F30%):  0.003

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.562
Plasma Protein Binding (PPB):  76.30717468261719%
Volume Distribution (VD):  1.397
Pgp-substrate:  9.799029350280762%

ADMET: Metabolism

CYP1A2-inhibitor:  0.637
CYP1A2-substrate:  0.656
CYP2C19-inhibitor:  0.853
CYP2C19-substrate:  0.908
CYP2C9-inhibitor:  0.378
CYP2C9-substrate:  0.513
CYP2D6-inhibitor:  0.053
CYP2D6-substrate:  0.846
CYP3A4-inhibitor:  0.867
CYP3A4-substrate:  0.463

ADMET: Excretion

Clearance (CL):  6.501
Half-life (T1/2):  0.124

ADMET: Toxicity

hERG Blockers:  0.013
Human Hepatotoxicity (H-HT):  0.409
Drug-inuced Liver Injury (DILI):  0.568
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.623
Maximum Recommended Daily Dose:  0.508
Skin Sensitization:  0.653
Carcinogencity:  0.818
Eye Corrosion:  0.009
Eye Irritation:  0.029
Respiratory Toxicity:  0.96

Download Data

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

  Natural Product: NPC476308

Natural Product ID:  NPC476308
Common Name*:   (1S*,3S*,4R*,7S*,8S*,12S*,13S*)-7-Formamidocycloamphilect-11(20)-Ene
IUPAC Name:   N-[(1S,3aR,4S,5aS,10aS,10bS,10cS)-1,4,7,7-tetramethyl-2,3,3a,4,5,5a,6,9,10,10a,10b,10c-dodecahydropyren-1-yl]formamide
Synonyms:  
Standard InCHIKey:  NYKQFGWZCBGFEZ-LKYYDDCCSA-N
Standard InCHI:  InChI=1S/C21H33NO/c1-13-9-15-11-20(2,3)10-14-5-6-17-19(18(14)15)16(13)7-8-21(17,4)22-12-23/h10,12-13,15-19H,5-9,11H2,1-4H3,(H,22,23)/t13-,15-,16+,17-,18-,19+,21-/m0/s1
SMILES:  CC1CC2CC(C=C3C2C4C1CCC(C4CC3)(C)NC=O)(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL563506
PubChem CID:   45268811
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0001093] Carboxylic acid derivatives
          • [CHEMONTID:0000475] Carboxylic acid amides
            • [CHEMONTID:0001663] Secondary carboxylic acid amides

*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
NPO33434 cymbastel hooperi Species n.a. n.a. n.a. n.a. n.a. PMID[19199790]

☑ 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
NPT6 Organism Plasmodium falciparum Plasmodium falciparum IC50 > 100.0 ug.mL-1 PMID[533064]

☑ 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 NPC476308 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
0.9429 High Similarity NPC476329
0.8873 High Similarity NPC138409
0.8857 High Similarity NPC476135
0.8429 Intermediate Similarity NPC476682
0.8356 Intermediate Similarity NPC184919
0.7867 Intermediate Similarity NPC472831
0.7746 Intermediate Similarity NPC317778
0.7534 Intermediate Similarity NPC145715
0.7534 Intermediate Similarity NPC89921
0.75 Intermediate Similarity NPC476288
0.7432 Intermediate Similarity NPC473959
0.726 Intermediate Similarity NPC311809
0.7222 Intermediate Similarity NPC324944
0.7183 Intermediate Similarity NPC318036
0.7126 Intermediate Similarity NPC152684
0.7123 Intermediate Similarity NPC28755
0.7123 Intermediate Similarity NPC152211
0.7083 Intermediate Similarity NPC470369
0.7083 Intermediate Similarity NPC173815
0.7083 Intermediate Similarity NPC470370
0.7037 Intermediate Similarity NPC476904
0.7013 Intermediate Similarity NPC37792
0.7 Intermediate Similarity NPC21773
0.6933 Remote Similarity NPC219621
0.6892 Remote Similarity NPC474454
0.6892 Remote Similarity NPC474420
0.6892 Remote Similarity NPC474455
0.6882 Remote Similarity NPC243985
0.6882 Remote Similarity NPC280710
0.6854 Remote Similarity NPC166458
0.6854 Remote Similarity NPC474458
0.6842 Remote Similarity NPC477740
0.6806 Remote Similarity NPC469770
0.6795 Remote Similarity NPC476039
0.6795 Remote Similarity NPC286669
0.6795 Remote Similarity NPC474456
0.6795 Remote Similarity NPC222366
0.679 Remote Similarity NPC265789
0.6782 Remote Similarity NPC283277
0.675 Remote Similarity NPC124384
0.6711 Remote Similarity NPC477739
0.6709 Remote Similarity NPC197805
0.6702 Remote Similarity NPC477290
0.6667 Remote Similarity NPC7214
0.6667 Remote Similarity NPC257962
0.6667 Remote Similarity NPC475724
0.6667 Remote Similarity NPC240650
0.6628 Remote Similarity NPC211322
0.6627 Remote Similarity NPC100334
0.6623 Remote Similarity NPC474435
0.6623 Remote Similarity NPC474027
0.6622 Remote Similarity NPC474415
0.6622 Remote Similarity NPC474528
0.6622 Remote Similarity NPC474457
0.6622 Remote Similarity NPC475696
0.6591 Remote Similarity NPC215474
0.6562 Remote Similarity NPC476903
0.6556 Remote Similarity NPC24733
0.6552 Remote Similarity NPC250632
0.6552 Remote Similarity NPC12035
0.6548 Remote Similarity NPC125828
0.6517 Remote Similarity NPC171639
0.65 Remote Similarity NPC474583
0.6495 Remote Similarity NPC167419
0.6484 Remote Similarity NPC157479
0.6477 Remote Similarity NPC329782
0.6471 Remote Similarity NPC265328
0.6471 Remote Similarity NPC106364
0.6471 Remote Similarity NPC120098
0.6471 Remote Similarity NPC122418
0.6471 Remote Similarity NPC27765
0.6471 Remote Similarity NPC290598
0.6471 Remote Similarity NPC30590
0.6456 Remote Similarity NPC163678
0.6452 Remote Similarity NPC249312
0.6447 Remote Similarity NPC475716
0.6447 Remote Similarity NPC472827
0.6429 Remote Similarity NPC17518
0.6429 Remote Similarity NPC22765
0.642 Remote Similarity NPC216460
0.642 Remote Similarity NPC32055
0.6404 Remote Similarity NPC224072
0.6404 Remote Similarity NPC472312
0.64 Remote Similarity NPC11130
0.64 Remote Similarity NPC471083
0.6395 Remote Similarity NPC472805
0.6395 Remote Similarity NPC101475
0.6395 Remote Similarity NPC90979
0.6395 Remote Similarity NPC157996
0.6395 Remote Similarity NPC34177
0.6395 Remote Similarity NPC40394
0.6374 Remote Similarity NPC182106
0.6374 Remote Similarity NPC311769
0.6374 Remote Similarity NPC75810
0.6374 Remote Similarity NPC147513
0.6373 Remote Similarity NPC55462
0.6353 Remote Similarity NPC34700
0.6353 Remote Similarity NPC138374
0.6344 Remote Similarity NPC259252
0.6337 Remote Similarity NPC45365
0.6337 Remote Similarity NPC293299
0.6333 Remote Similarity NPC21667
0.6327 Remote Similarity NPC474164
0.6327 Remote Similarity NPC184033
0.6322 Remote Similarity NPC98386
0.6322 Remote Similarity NPC22955
0.6322 Remote Similarity NPC474989
0.6322 Remote Similarity NPC230295
0.6322 Remote Similarity NPC470396
0.6322 Remote Similarity NPC300499
0.6322 Remote Similarity NPC196753
0.6322 Remote Similarity NPC79704
0.6322 Remote Similarity NPC99168
0.6322 Remote Similarity NPC253807
0.6322 Remote Similarity NPC158662
0.6311 Remote Similarity NPC25340
0.631 Remote Similarity NPC182717
0.631 Remote Similarity NPC474743
0.631 Remote Similarity NPC471799
0.6304 Remote Similarity NPC56107
0.6292 Remote Similarity NPC152039
0.6292 Remote Similarity NPC118329
0.6289 Remote Similarity NPC311164
0.6289 Remote Similarity NPC272732
0.6265 Remote Similarity NPC145498
0.6263 Remote Similarity NPC91604
0.625 Remote Similarity NPC291379
0.625 Remote Similarity NPC53744
0.6238 Remote Similarity NPC50815
0.6238 Remote Similarity NPC247060
0.6235 Remote Similarity NPC471797
0.6222 Remote Similarity NPC39966
0.622 Remote Similarity NPC39157
0.622 Remote Similarity NPC82477
0.622 Remote Similarity NPC296697
0.622 Remote Similarity NPC208999
0.622 Remote Similarity NPC94192
0.622 Remote Similarity NPC142754
0.622 Remote Similarity NPC160209
0.6203 Remote Similarity NPC475755
0.62 Remote Similarity NPC275686
0.619 Remote Similarity NPC242001
0.618 Remote Similarity NPC295131
0.6176 Remote Similarity NPC241879
0.6173 Remote Similarity NPC149680
0.617 Remote Similarity NPC34754
0.617 Remote Similarity NPC324405
0.6164 Remote Similarity NPC212905
0.6163 Remote Similarity NPC230301
0.6163 Remote Similarity NPC22105
0.6163 Remote Similarity NPC134847
0.6163 Remote Similarity NPC136188
0.6163 Remote Similarity NPC285893
0.6163 Remote Similarity NPC257347
0.6163 Remote Similarity NPC304309
0.6163 Remote Similarity NPC162742
0.6163 Remote Similarity NPC141071
0.6163 Remote Similarity NPC288035
0.6163 Remote Similarity NPC471723
0.6163 Remote Similarity NPC28657
0.6162 Remote Similarity NPC140300
0.6146 Remote Similarity NPC476064
0.6145 Remote Similarity NPC286814
0.6145 Remote Similarity NPC245223
0.6136 Remote Similarity NPC72507
0.6132 Remote Similarity NPC472359
0.6117 Remote Similarity NPC119329
0.6111 Remote Similarity NPC242350
0.6111 Remote Similarity NPC3915
0.61 Remote Similarity NPC140685
0.6098 Remote Similarity NPC220210
0.6098 Remote Similarity NPC68703
0.6098 Remote Similarity NPC69649
0.6098 Remote Similarity NPC20181
0.6095 Remote Similarity NPC159367
0.6092 Remote Similarity NPC244488
0.6092 Remote Similarity NPC470749
0.6092 Remote Similarity NPC240604
0.6092 Remote Similarity NPC237460
0.6092 Remote Similarity NPC247325
0.6092 Remote Similarity NPC129165
0.6092 Remote Similarity NPC113733
0.6092 Remote Similarity NPC134330
0.6092 Remote Similarity NPC112680
0.6092 Remote Similarity NPC189883
0.6092 Remote Similarity NPC321381
0.6092 Remote Similarity NPC300324
0.6092 Remote Similarity NPC321016
0.6092 Remote Similarity NPC107059
0.6087 Remote Similarity NPC477289
0.6082 Remote Similarity NPC476752
0.6082 Remote Similarity NPC476753
0.6081 Remote Similarity NPC474416
0.6078 Remote Similarity NPC226509
0.6078 Remote Similarity NPC152718
0.6078 Remote Similarity NPC176012
0.6076 Remote Similarity NPC469728
0.6071 Remote Similarity NPC475728
0.6071 Remote Similarity NPC34834
0.6058 Remote Similarity NPC258130

  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 NPC476308 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
0.6667 Remote Similarity NPD6939 Phase 2
0.6667 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6526 Remote Similarity NPD5771 Approved
0.6436 Remote Similarity NPD7812 Clinical (unspecified phase)
0.6354 Remote Similarity NPD5769 Clinical (unspecified phase)
0.625 Remote Similarity NPD7645 Phase 2
0.619 Remote Similarity NPD5365 Phase 2
0.6163 Remote Similarity NPD7339 Approved
0.6163 Remote Similarity NPD6942 Approved
0.6 Remote Similarity NPD4243 Approved
0.5909 Remote Similarity NPD3701 Clinical (unspecified phase)
0.59 Remote Similarity NPD2895 Discontinued
0.5862 Remote Similarity NPD4785 Approved
0.5862 Remote Similarity NPD4784 Approved
0.5824 Remote Similarity NPD7525 Registered
0.5765 Remote Similarity NPD6923 Approved
0.5765 Remote Similarity NPD6922 Approved
0.5761 Remote Similarity NPD8028 Phase 2
0.5698 Remote Similarity NPD7144 Approved
0.5698 Remote Similarity NPD7143 Approved
0.567 Remote Similarity NPD4722 Approved
0.567 Remote Similarity NPD4723 Approved
0.5647 Remote Similarity NPD3621 Clinical (unspecified phase)
0.5641 Remote Similarity NPD4219 Approved
0.5632 Remote Similarity NPD7152 Approved
0.5632 Remote Similarity NPD7150 Approved
0.5632 Remote Similarity NPD7151 Approved
0.5618 Remote Similarity NPD4190 Phase 3
0.5618 Remote Similarity NPD5275 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