Structure

Physi-Chem Properties

Molecular Weight:  319.21
Volume:  340.969
LogP:  4.933
LogD:  4.209
LogS:  -5.179
# Rotatable Bonds:  7
TPSA:  55.4
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  3
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.444
Synthetic Accessibility Score:  4.419
Fsp3:  0.789
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:  -4.72
MDCK Permeability:  3.075549102504738e-05
Pgp-inhibitor:  0.966
Pgp-substrate:  0.002
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.617
30% Bioavailability (F30%):  0.384

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.631
Plasma Protein Binding (PPB):  96.58715057373047%
Volume Distribution (VD):  1.217
Pgp-substrate:  2.7940287590026855%

ADMET: Metabolism

CYP1A2-inhibitor:  0.185
CYP1A2-substrate:  0.681
CYP2C19-inhibitor:  0.873
CYP2C19-substrate:  0.822
CYP2C9-inhibitor:  0.74
CYP2C9-substrate:  0.312
CYP2D6-inhibitor:  0.017
CYP2D6-substrate:  0.125
CYP3A4-inhibitor:  0.939
CYP3A4-substrate:  0.515

ADMET: Excretion

Clearance (CL):  4.263
Half-life (T1/2):  0.159

ADMET: Toxicity

hERG Blockers:  0.016
Human Hepatotoxicity (H-HT):  0.117
Drug-inuced Liver Injury (DILI):  0.128
AMES Toxicity:  0.188
Rat Oral Acute Toxicity:  0.667
Maximum Recommended Daily Dose:  0.342
Skin Sensitization:  0.512
Carcinogencity:  0.819
Eye Corrosion:  0.026
Eye Irritation:  0.039
Respiratory Toxicity:  0.485

Download Data

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

  Natural Product: NPC123141

Natural Product ID:  NPC123141
Common Name*:   Cinnabaramide C
IUPAC Name:   (1S,2R,5R)-5-[[(1R)-cyclohex-2-en-1-yl]methyl]-2-hexyl-1-methyl-7-oxa-4-azabicyclo[3.2.0]heptane-3,6-dione
Synonyms:   Cinnabaramide C
Standard InCHIKey:  HRIJMKFCVROBTA-PDWMJMLSSA-N
Standard InCHI:  InChI=1S/C19H29NO3/c1-3-4-5-9-12-15-16(21)20-19(17(22)23-18(15,19)2)13-14-10-7-6-8-11-14/h7,10,14-15H,3-6,8-9,11-13H2,1-2H3,(H,20,21)/t14-,15+,18+,19+/m1/s1
SMILES:  CCCCCC[C@H]1C(=N[C@@]2(C[C@@H]3C=CCCC3)C(=O)O[C@@]12C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL221018
PubChem CID:   9973253
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives

*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
NPO32890 terrestrial streptomycete Species n.a. n.a. n.a. n.a. n.a. PMID[17249727]

☑ 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
NPT24354 PROTEIN COMPLEX 20S proteasome Homo sapiens IC50 = 12.0 nM PMID[482632]
NPT35 Others n.a. Stability = 50.0 % PMID[482632]

☑ 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 NPC123141 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
0.9271 High Similarity NPC14537
0.9175 High Similarity NPC473252
0.875 High Similarity NPC234542
0.866 High Similarity NPC473224
0.8544 High Similarity NPC12270
0.7818 Intermediate Similarity NPC201968
0.7636 Intermediate Similarity NPC50694
0.7157 Intermediate Similarity NPC226513
0.6726 Remote Similarity NPC474725
0.6696 Remote Similarity NPC475800
0.6607 Remote Similarity NPC472615
0.6604 Remote Similarity NPC477290
0.6577 Remote Similarity NPC474563
0.6577 Remote Similarity NPC215988
0.6571 Remote Similarity NPC314500
0.6518 Remote Similarity NPC472616
0.6505 Remote Similarity NPC472614
0.6491 Remote Similarity NPC70235
0.6486 Remote Similarity NPC469598
0.646 Remote Similarity NPC271269
0.6441 Remote Similarity NPC476814
0.6441 Remote Similarity NPC471645
0.6441 Remote Similarity NPC476813
0.6435 Remote Similarity NPC473578
0.6408 Remote Similarity NPC475753
0.6381 Remote Similarity NPC159369
0.6381 Remote Similarity NPC39290
0.6348 Remote Similarity NPC307903
0.6348 Remote Similarity NPC140251
0.6348 Remote Similarity NPC475150
0.6337 Remote Similarity NPC474312
0.6327 Remote Similarity NPC240170
0.6327 Remote Similarity NPC120776
0.6316 Remote Similarity NPC154601
0.6273 Remote Similarity NPC4834
0.6271 Remote Similarity NPC469865
0.6263 Remote Similarity NPC218817
0.6263 Remote Similarity NPC11796
0.6261 Remote Similarity NPC251330
0.6239 Remote Similarity NPC127578
0.6228 Remote Similarity NPC119329
0.6228 Remote Similarity NPC74035
0.6226 Remote Similarity NPC256902
0.6226 Remote Similarity NPC118193
0.6224 Remote Similarity NPC469514
0.621 Remote Similarity NPC80150
0.6204 Remote Similarity NPC472613
0.619 Remote Similarity NPC171722
0.6186 Remote Similarity NPC55527
0.6176 Remote Similarity NPC47135
0.6174 Remote Similarity NPC475918
0.617 Remote Similarity NPC476614
0.6162 Remote Similarity NPC281296
0.6162 Remote Similarity NPC107668
0.6154 Remote Similarity NPC329305
0.6154 Remote Similarity NPC133729
0.6142 Remote Similarity NPC204556
0.6126 Remote Similarity NPC475438
0.6111 Remote Similarity NPC472264
0.6111 Remote Similarity NPC472705
0.6105 Remote Similarity NPC199557
0.6102 Remote Similarity NPC113012
0.6102 Remote Similarity NPC122926
0.6102 Remote Similarity NPC46764
0.61 Remote Similarity NPC121200
0.6095 Remote Similarity NPC258824
0.6083 Remote Similarity NPC469597
0.6082 Remote Similarity NPC167145
0.6075 Remote Similarity NPC97577
0.6066 Remote Similarity NPC147707
0.6066 Remote Similarity NPC188010
0.6066 Remote Similarity NPC471117
0.6066 Remote Similarity NPC471120
0.6064 Remote Similarity NPC60120
0.6058 Remote Similarity NPC295799
0.605 Remote Similarity NPC474411
0.605 Remote Similarity NPC474431
0.6048 Remote Similarity NPC310467
0.6044 Remote Similarity NPC174560
0.6044 Remote Similarity NPC125312
0.604 Remote Similarity NPC469617
0.6038 Remote Similarity NPC86005
0.6036 Remote Similarity NPC469369
0.6036 Remote Similarity NPC469528
0.6036 Remote Similarity NPC165332
0.6036 Remote Similarity NPC180722
0.6036 Remote Similarity NPC195645
0.6036 Remote Similarity NPC121857
0.6034 Remote Similarity NPC101106
0.6034 Remote Similarity NPC135216
0.602 Remote Similarity NPC330016
0.6019 Remote Similarity NPC17143
0.6019 Remote Similarity NPC474964
0.6019 Remote Similarity NPC477288
0.6019 Remote Similarity NPC15059
0.6019 Remote Similarity NPC47230
0.6016 Remote Similarity NPC471118
0.6016 Remote Similarity NPC471121
0.6016 Remote Similarity NPC9714
0.6 Remote Similarity NPC145898
0.6 Remote Similarity NPC23963
0.6 Remote Similarity NPC469515
0.6 Remote Similarity NPC473314
0.6 Remote Similarity NPC7797
0.6 Remote Similarity NPC125290
0.5982 Remote Similarity NPC167380
0.598 Remote Similarity NPC103634
0.598 Remote Similarity NPC200446
0.5978 Remote Similarity NPC316674
0.5969 Remote Similarity NPC477793
0.5969 Remote Similarity NPC329919
0.5968 Remote Similarity NPC169328
0.5966 Remote Similarity NPC476290
0.5965 Remote Similarity NPC474873
0.5963 Remote Similarity NPC36491
0.5963 Remote Similarity NPC476064
0.5962 Remote Similarity NPC477584
0.5962 Remote Similarity NPC477373
0.5962 Remote Similarity NPC471595
0.596 Remote Similarity NPC199445
0.5946 Remote Similarity NPC314009
0.5946 Remote Similarity NPC54905
0.5943 Remote Similarity NPC477994
0.5943 Remote Similarity NPC477993
0.5941 Remote Similarity NPC469495
0.5941 Remote Similarity NPC474833
0.5941 Remote Similarity NPC469492
0.5941 Remote Similarity NPC179028
0.5941 Remote Similarity NPC321514
0.5935 Remote Similarity NPC316325
0.5932 Remote Similarity NPC287572
0.5932 Remote Similarity NPC471636
0.5929 Remote Similarity NPC244411
0.5922 Remote Similarity NPC117960
0.5922 Remote Similarity NPC325031
0.5922 Remote Similarity NPC327002
0.5922 Remote Similarity NPC14044
0.5922 Remote Similarity NPC172309
0.5913 Remote Similarity NPC128501
0.5909 Remote Similarity NPC115021
0.5902 Remote Similarity NPC470540
0.59 Remote Similarity NPC474447
0.59 Remote Similarity NPC110461
0.59 Remote Similarity NPC12740
0.59 Remote Similarity NPC61863
0.5893 Remote Similarity NPC476449
0.5893 Remote Similarity NPC9812
0.5888 Remote Similarity NPC477959
0.5882 Remote Similarity NPC24389
0.5882 Remote Similarity NPC82488
0.5882 Remote Similarity NPC308545
0.5882 Remote Similarity NPC113363
0.5882 Remote Similarity NPC469517
0.5882 Remote Similarity NPC209995
0.5882 Remote Similarity NPC474891
0.5877 Remote Similarity NPC54705
0.5872 Remote Similarity NPC473448
0.5868 Remote Similarity NPC476269
0.5868 Remote Similarity NPC1111
0.5868 Remote Similarity NPC261750
0.5865 Remote Similarity NPC76999
0.5865 Remote Similarity NPC474252
0.5859 Remote Similarity NPC474551
0.5859 Remote Similarity NPC251970
0.5859 Remote Similarity NPC283908
0.5859 Remote Similarity NPC469494
0.5859 Remote Similarity NPC241854
0.5859 Remote Similarity NPC472966
0.5859 Remote Similarity NPC103958
0.5859 Remote Similarity NPC476046
0.5859 Remote Similarity NPC183503
0.5859 Remote Similarity NPC161923
0.5856 Remote Similarity NPC5418
0.5849 Remote Similarity NPC76333
0.5847 Remote Similarity NPC250187
0.5841 Remote Similarity NPC476344
0.5841 Remote Similarity NPC53844
0.584 Remote Similarity NPC323532
0.5833 Remote Similarity NPC474812
0.5833 Remote Similarity NPC193386
0.5833 Remote Similarity NPC314050
0.5833 Remote Similarity NPC315809
0.5827 Remote Similarity NPC478015
0.5827 Remote Similarity NPC478014
0.5827 Remote Similarity NPC478016
0.5826 Remote Similarity NPC175531
0.5826 Remote Similarity NPC62670
0.5826 Remote Similarity NPC116139
0.5825 Remote Similarity NPC233377
0.5825 Remote Similarity NPC469920
0.5821 Remote Similarity NPC75318
0.582 Remote Similarity NPC106479
0.5818 Remote Similarity NPC300312
0.5818 Remote Similarity NPC177037
0.5818 Remote Similarity NPC111114
0.5818 Remote Similarity NPC472814
0.5818 Remote Similarity NPC261607
0.5816 Remote Similarity NPC126061
0.5816 Remote Similarity NPC160817
0.5816 Remote Similarity NPC320119

  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 NPC123141 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
0.8544 High Similarity NPD1719 Phase 1
0.6771 Remote Similarity NPD3732 Approved
0.6667 Remote Similarity NPD5781 Clinical (unspecified phase)
0.6522 Remote Similarity NPD6420 Discontinued
0.6412 Remote Similarity NPD6333 Approved
0.6412 Remote Similarity NPD6334 Approved
0.6379 Remote Similarity NPD6421 Discontinued
0.6182 Remote Similarity NPD4228 Discovery
0.6176 Remote Similarity NPD7345 Approved
0.6161 Remote Similarity NPD6404 Discontinued
0.6154 Remote Similarity NPD6413 Approved
0.6078 Remote Similarity NPD5369 Approved
0.6078 Remote Similarity NPD1448 Clinical (unspecified phase)
0.6078 Remote Similarity NPD857 Phase 3
0.6075 Remote Similarity NPD6101 Approved
0.6075 Remote Similarity NPD5764 Clinical (unspecified phase)
0.6055 Remote Similarity NPD5778 Approved
0.6055 Remote Similarity NPD5779 Approved
0.6036 Remote Similarity NPD7839 Suspended
0.6034 Remote Similarity NPD4211 Phase 1
0.6019 Remote Similarity NPD6435 Approved
0.6 Remote Similarity NPD6914 Discontinued
0.5963 Remote Similarity NPD6411 Approved
0.5935 Remote Similarity NPD7500 Approved
0.5917 Remote Similarity NPD3644 Approved
0.5917 Remote Similarity NPD3642 Approved
0.5917 Remote Similarity NPD3643 Approved
0.5891 Remote Similarity NPD8074 Phase 3
0.5833 Remote Similarity NPD4264 Clinical (unspecified phase)
0.5825 Remote Similarity NPD5368 Approved
0.5794 Remote Similarity NPD5786 Approved
0.5789 Remote Similarity NPD7331 Phase 2
0.5785 Remote Similarity NPD2204 Approved
0.5772 Remote Similarity NPD2652 Approved
0.5772 Remote Similarity NPD2650 Approved
0.5752 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5714 Remote Similarity NPD4269 Approved
0.5714 Remote Similarity NPD4270 Approved
0.5691 Remote Similarity NPD1376 Discontinued
0.5676 Remote Similarity NPD7983 Approved
0.566 Remote Similarity NPD7154 Phase 3
0.5657 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5656 Remote Similarity NPD7116 Clinical (unspecified phase)
0.5631 Remote Similarity NPD7917 Clinical (unspecified phase)
0.5631 Remote Similarity NPD7918 Clinical (unspecified phase)
0.5625 Remote Similarity NPD5981 Approved
0.5615 Remote Similarity NPD8340 Approved
0.5615 Remote Similarity NPD8341 Approved
0.5615 Remote Similarity NPD8299 Approved
0.5615 Remote Similarity NPD8342 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