Structure

Physi-Chem Properties

Molecular Weight:  355.21
Volume:  361.267
LogP:  2.174
LogD:  2.369
LogS:  -4.651
# Rotatable Bonds:  0
TPSA:  38.77
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  9
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.626
Synthetic Accessibility Score:  7.45
Fsp3:  0.864
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  2
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.984
MDCK Permeability:  3.130162076558918e-05
Pgp-inhibitor:  0.017
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.927
30% Bioavailability (F30%):  0.949

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.756
Plasma Protein Binding (PPB):  54.98139190673828%
Volume Distribution (VD):  2.175
Pgp-substrate:  58.07371139526367%

ADMET: Metabolism

CYP1A2-inhibitor:  0.036
CYP1A2-substrate:  0.889
CYP2C19-inhibitor:  0.055
CYP2C19-substrate:  0.728
CYP2C9-inhibitor:  0.074
CYP2C9-substrate:  0.034
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.537
CYP3A4-inhibitor:  0.487
CYP3A4-substrate:  0.346

ADMET: Excretion

Clearance (CL):  7.539
Half-life (T1/2):  0.365

ADMET: Toxicity

hERG Blockers:  0.232
Human Hepatotoxicity (H-HT):  0.153
Drug-inuced Liver Injury (DILI):  0.152
AMES Toxicity:  0.026
Rat Oral Acute Toxicity:  0.893
Maximum Recommended Daily Dose:  0.936
Skin Sensitization:  0.927
Carcinogencity:  0.362
Eye Corrosion:  0.019
Eye Irritation:  0.023
Respiratory Toxicity:  0.984

Download Data

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

  Natural Product: NPC477963

Natural Product ID:  NPC477963
Common Name*:   (1R,2R,5S,7S,8S,12R,18S,21R)-12-methyl-4-methylidene-14,19-dioxa-17-azaheptacyclo[10.7.2.22,5.02,7.08,18.08,21.013,17]tricosan-3-one
IUPAC Name:   (1R,2R,5S,7S,8S,12R,18S,21R)-12-methyl-4-methylidene-14,19-dioxa-17-azaheptacyclo[10.7.2.22,5.02,7.08,18.08,21.013,17]tricosan-3-one
Synonyms:  
Standard InCHIKey:  LEZMMRATPABCNQ-LEUZYGODSA-N
Standard InCHI:  InChI=1S/C22H29NO3/c1-12-13-4-7-22(17(12)24)15(10-13)21-6-3-5-20(2)14(21)11-16(22)26-19(21)23-8-9-25-18(20)23/h13-16,18-19H,1,3-11H2,2H3/t13-,14+,15-,16+,18?,19-,20+,21-,22+/m0/s1
SMILES:  C[C@@]12CCC[C@]34[C@@H]1C[C@H]([C@]56[C@H]3C[C@H](CC5)C(=C)C6=O)O[C@@H]4N7C2OCC7
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   90671719
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003401] Villanovane, atisane, trachylobane or helvifulvane diterpenoids
            • [CHEMONTID:0002738] Atisane diterpenoids

*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
NPO6485 Spiraea japonica Species Rosaceae Eukaryota n.a. n.a. n.a. PMID[24684844]
NPO6485 Spiraea japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO6485 Spiraea japonica Species Rosaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO6485 Spiraea japonica Species Rosaceae 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
NPT1893 Cell Line MEF Mus musculus IC50 = 2243 nM PMID[24684844]
NPT660 Cell Line SW480 Homo sapiens Activity = 15.9 % PMID[24684844]
NPT660 Cell Line SW480 Homo sapiens Activity = 16.9 % PMID[24684844]
NPT660 Cell Line SW480 Homo sapiens Activity = 18.2 % PMID[24684844]
NPT1893 Cell Line MEF Mus musculus Activity = 86.2 % PMID[24684844]
NPT1893 Cell Line MEF Mus musculus Activity = 1.9 % PMID[24684844]
NPT1893 Cell Line MEF Mus musculus Activity = 87.8 % PMID[24684844]
NPT116 Cell Line HL-60 Homo sapiens IC50 = 1340 nM PMID[24684844]
NPT659 Cell Line SMMC-7721 Homo sapiens IC50 = 1040 nM PMID[24684844]
NPT81 Cell Line A549 Homo sapiens IC50 = 2030 nM PMID[24684844]
NPT83 Cell Line MCF7 Homo sapiens IC50 = 670 nM PMID[24684844]
NPT660 Cell Line SW480 Homo sapiens IC50 = 1970 nM PMID[24684844]

☑ 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 NPC477963 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
0.6992 Remote Similarity NPC135431
0.6935 Remote Similarity NPC209252
0.6875 Remote Similarity NPC476934
0.6875 Remote Similarity NPC470230
0.6847 Remote Similarity NPC471043
0.6754 Remote Similarity NPC475118
0.6696 Remote Similarity NPC470232
0.6696 Remote Similarity NPC470229
0.6695 Remote Similarity NPC14634
0.6667 Remote Similarity NPC238323
0.6667 Remote Similarity NPC259009
0.6667 Remote Similarity NPC475239
0.6641 Remote Similarity NPC321197
0.6639 Remote Similarity NPC475803
0.6639 Remote Similarity NPC309388
0.6638 Remote Similarity NPC329910
0.6636 Remote Similarity NPC190704
0.6636 Remote Similarity NPC471034
0.6609 Remote Similarity NPC47853
0.6609 Remote Similarity NPC470385
0.6609 Remote Similarity NPC470386
0.6587 Remote Similarity NPC145501
0.6585 Remote Similarity NPC218602
0.6583 Remote Similarity NPC139347
0.6581 Remote Similarity NPC96839
0.656 Remote Similarity NPC124358
0.6529 Remote Similarity NPC202793
0.6529 Remote Similarity NPC474558
0.6525 Remote Similarity NPC220111
0.6525 Remote Similarity NPC471038
0.6525 Remote Similarity NPC474793
0.6514 Remote Similarity NPC476935
0.6496 Remote Similarity NPC470387
0.6491 Remote Similarity NPC80401
0.6475 Remote Similarity NPC130511
0.6475 Remote Similarity NPC4115
0.6475 Remote Similarity NPC56656
0.6475 Remote Similarity NPC307660
0.6475 Remote Similarity NPC12823
0.6471 Remote Similarity NPC287676
0.6471 Remote Similarity NPC267921
0.6455 Remote Similarity NPC291320
0.6455 Remote Similarity NPC471036
0.6435 Remote Similarity NPC476168
0.6435 Remote Similarity NPC198242
0.6435 Remote Similarity NPC211403
0.6435 Remote Similarity NPC299185
0.6429 Remote Similarity NPC145625
0.6429 Remote Similarity NPC157929
0.6423 Remote Similarity NPC471461
0.6423 Remote Similarity NPC471474
0.6423 Remote Similarity NPC469746
0.6423 Remote Similarity NPC186054
0.6423 Remote Similarity NPC67745
0.6417 Remote Similarity NPC289148
0.6417 Remote Similarity NPC236585
0.6417 Remote Similarity NPC46848
0.6417 Remote Similarity NPC52899
0.6417 Remote Similarity NPC163963
0.6397 Remote Similarity NPC478139
0.6393 Remote Similarity NPC244247
0.6393 Remote Similarity NPC13149
0.6387 Remote Similarity NPC78427
0.6387 Remote Similarity NPC109059
0.6387 Remote Similarity NPC16911
0.6387 Remote Similarity NPC288
0.6379 Remote Similarity NPC181594
0.6379 Remote Similarity NPC144739
0.6378 Remote Similarity NPC471248
0.6378 Remote Similarity NPC94141
0.6372 Remote Similarity NPC153604
0.6372 Remote Similarity NPC175293
0.6371 Remote Similarity NPC469733
0.6371 Remote Similarity NPC89860
0.6371 Remote Similarity NPC55973
0.6371 Remote Similarity NPC469984
0.6371 Remote Similarity NPC63841
0.6371 Remote Similarity NPC232133
0.6371 Remote Similarity NPC469729
0.6371 Remote Similarity NPC189663
0.6371 Remote Similarity NPC473410
0.6371 Remote Similarity NPC471094
0.6364 Remote Similarity NPC304832
0.6364 Remote Similarity NPC88203
0.6364 Remote Similarity NPC246736
0.6364 Remote Similarity NPC275990
0.6364 Remote Similarity NPC476755
0.6364 Remote Similarity NPC214946
0.6364 Remote Similarity NPC76866
0.6364 Remote Similarity NPC286519
0.6364 Remote Similarity NPC148628
0.6356 Remote Similarity NPC165616
0.6356 Remote Similarity NPC200054
0.6356 Remote Similarity NPC29410
0.6348 Remote Similarity NPC261994
0.6348 Remote Similarity NPC312637
0.6348 Remote Similarity NPC470378
0.6348 Remote Similarity NPC149761
0.6338 Remote Similarity NPC172365
0.6338 Remote Similarity NPC82931
0.6338 Remote Similarity NPC210729
0.6333 Remote Similarity NPC470388
0.6328 Remote Similarity NPC17165
0.6325 Remote Similarity NPC104371
0.6325 Remote Similarity NPC224410
0.6325 Remote Similarity NPC289539
0.6325 Remote Similarity NPC100257
0.6325 Remote Similarity NPC215271
0.6325 Remote Similarity NPC129004
0.6325 Remote Similarity NPC191094
0.6325 Remote Similarity NPC302008
0.6325 Remote Similarity NPC261333
0.6325 Remote Similarity NPC153775
0.6325 Remote Similarity NPC292374
0.6325 Remote Similarity NPC111524
0.6325 Remote Similarity NPC91772
0.6325 Remote Similarity NPC101233
0.6325 Remote Similarity NPC29247
0.632 Remote Similarity NPC274827
0.632 Remote Similarity NPC469983
0.632 Remote Similarity NPC469744
0.632 Remote Similarity NPC252679
0.632 Remote Similarity NPC274895
0.632 Remote Similarity NPC118721
0.632 Remote Similarity NPC102741
0.632 Remote Similarity NPC131903
0.6311 Remote Similarity NPC266
0.6311 Remote Similarity NPC122811
0.6311 Remote Similarity NPC96217
0.6311 Remote Similarity NPC277074
0.6311 Remote Similarity NPC216114
0.6311 Remote Similarity NPC209298
0.6311 Remote Similarity NPC87927
0.6303 Remote Similarity NPC469810
0.6299 Remote Similarity NPC476964
0.6296 Remote Similarity NPC96010
0.6296 Remote Similarity NPC280903
0.6296 Remote Similarity NPC317654
0.6293 Remote Similarity NPC250753
0.629 Remote Similarity NPC176773
0.629 Remote Similarity NPC88833
0.629 Remote Similarity NPC96333
0.629 Remote Similarity NPC61071
0.6283 Remote Similarity NPC471042
0.6281 Remote Similarity NPC148279
0.6281 Remote Similarity NPC471790
0.6279 Remote Similarity NPC229752
0.6279 Remote Similarity NPC470538
0.6271 Remote Similarity NPC41070
0.6271 Remote Similarity NPC84018
0.6271 Remote Similarity NPC98639
0.6271 Remote Similarity NPC138245
0.6271 Remote Similarity NPC231060
0.627 Remote Similarity NPC470532
0.627 Remote Similarity NPC471476
0.627 Remote Similarity NPC470531
0.627 Remote Similarity NPC471093
0.627 Remote Similarity NPC85391
0.627 Remote Similarity NPC470528
0.627 Remote Similarity NPC470527
0.627 Remote Similarity NPC470530
0.627 Remote Similarity NPC470533
0.627 Remote Similarity NPC137104
0.627 Remote Similarity NPC470529
0.627 Remote Similarity NPC473324
0.627 Remote Similarity NPC320383
0.627 Remote Similarity NPC474786
0.6269 Remote Similarity NPC476503
0.626 Remote Similarity NPC101842
0.626 Remote Similarity NPC98603
0.626 Remote Similarity NPC84928
0.626 Remote Similarity NPC212874
0.625 Remote Similarity NPC475394
0.625 Remote Similarity NPC162459
0.625 Remote Similarity NPC98837
0.625 Remote Similarity NPC475584
0.625 Remote Similarity NPC475152
0.625 Remote Similarity NPC26270
0.625 Remote Similarity NPC38296
0.625 Remote Similarity NPC38471
0.625 Remote Similarity NPC20479
0.625 Remote Similarity NPC478136
0.625 Remote Similarity NPC89099
0.625 Remote Similarity NPC146683
0.625 Remote Similarity NPC28224
0.625 Remote Similarity NPC106479
0.625 Remote Similarity NPC477352
0.625 Remote Similarity NPC28864
0.6231 Remote Similarity NPC78836
0.6228 Remote Similarity NPC165895
0.6228 Remote Similarity NPC57469
0.622 Remote Similarity NPC329953
0.622 Remote Similarity NPC213320
0.622 Remote Similarity NPC122339
0.622 Remote Similarity NPC29505
0.622 Remote Similarity NPC63244
0.6218 Remote Similarity NPC317573
0.6218 Remote Similarity NPC135548
0.6218 Remote Similarity NPC140242
0.6218 Remote Similarity NPC264979

  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 NPC477963 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
0.6496 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6475 Remote Similarity NPD6920 Discontinued
0.6429 Remote Similarity NPD8077 Approved
0.6429 Remote Similarity NPD8078 Approved
0.6341 Remote Similarity NPD8040 Discontinued
0.624 Remote Similarity NPD6415 Discontinued
0.6179 Remote Similarity NPD7986 Approved
0.6179 Remote Similarity NPD7987 Approved
0.6179 Remote Similarity NPD7912 Approved
0.6179 Remote Similarity NPD7911 Approved
0.6165 Remote Similarity NPD6909 Approved
0.6165 Remote Similarity NPD6908 Approved
0.6154 Remote Similarity NPD7754 Approved
0.6154 Remote Similarity NPD7755 Approved
0.6131 Remote Similarity NPD8336 Approved
0.6131 Remote Similarity NPD8337 Approved
0.6045 Remote Similarity NPD6921 Approved
0.6032 Remote Similarity NPD7646 Clinical (unspecified phase)
0.6032 Remote Similarity NPD7990 Approved
0.6032 Remote Similarity NPD7989 Approved
0.5957 Remote Similarity NPD8338 Approved
0.5948 Remote Similarity NPD3573 Approved
0.5917 Remote Similarity NPD7748 Approved
0.5917 Remote Similarity NPD7900 Approved
0.5917 Remote Similarity NPD7901 Clinical (unspecified phase)
0.5862 Remote Similarity NPD6333 Approved
0.5862 Remote Similarity NPD6334 Approved
0.5845 Remote Similarity NPD6845 Suspended
0.5827 Remote Similarity NPD7333 Discontinued
0.5827 Remote Similarity NPD6008 Approved
0.5778 Remote Similarity NPD7517 Approved
0.5778 Remote Similarity NPD7519 Approved
0.5778 Remote Similarity NPD7518 Approved
0.5776 Remote Similarity NPD7520 Clinical (unspecified phase)
0.5772 Remote Similarity NPD7902 Approved
0.5763 Remote Similarity NPD7513 Clinical (unspecified phase)
0.575 Remote Similarity NPD8035 Phase 2
0.575 Remote Similarity NPD7515 Phase 2
0.575 Remote Similarity NPD6079 Approved
0.575 Remote Similarity NPD8034 Phase 2
0.5738 Remote Similarity NPD7991 Discontinued
0.5726 Remote Similarity NPD3618 Phase 1
0.5726 Remote Similarity NPD8308 Discontinued
0.5725 Remote Similarity NPD8328 Phase 3
0.5724 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5328 Approved
0.5704 Remote Similarity NPD6914 Discontinued
0.5655 Remote Similarity NPD8415 Approved
0.5639 Remote Similarity NPD8133 Approved
0.5625 Remote Similarity NPD8449 Approved
0.562 Remote Similarity NPD6054 Approved
0.5612 Remote Similarity NPD7122 Discontinued
0.5603 Remote Similarity NPD4788 Approved
0.56 Remote Similarity NPD7638 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