Structure

Physi-Chem Properties

Molecular Weight:  371.25
Volume:  393.04
LogP:  4.051
LogD:  2.773
LogS:  -3.377
# Rotatable Bonds:  3
TPSA:  38.77
# H-Bond Aceptor:  4
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.545
Synthetic Accessibility Score:  6.348
Fsp3:  0.783
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.929
MDCK Permeability:  1.913636333483737e-05
Pgp-inhibitor:  0.011
Pgp-substrate:  0.215
Human Intestinal Absorption (HIA):  0.003
20% Bioavailability (F20%):  0.36
30% Bioavailability (F30%):  0.987

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.992
Plasma Protein Binding (PPB):  55.037628173828125%
Volume Distribution (VD):  2.673
Pgp-substrate:  33.9332389831543%

ADMET: Metabolism

CYP1A2-inhibitor:  0.05
CYP1A2-substrate:  0.369
CYP2C19-inhibitor:  0.123
CYP2C19-substrate:  0.949
CYP2C9-inhibitor:  0.07
CYP2C9-substrate:  0.095
CYP2D6-inhibitor:  0.68
CYP2D6-substrate:  0.889
CYP3A4-inhibitor:  0.921
CYP3A4-substrate:  0.899

ADMET: Excretion

Clearance (CL):  14.447
Half-life (T1/2):  0.046

ADMET: Toxicity

hERG Blockers:  0.923
Human Hepatotoxicity (H-HT):  0.688
Drug-inuced Liver Injury (DILI):  0.337
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.235
Maximum Recommended Daily Dose:  0.957
Skin Sensitization:  0.879
Carcinogencity:  0.801
Eye Corrosion:  0.003
Eye Irritation:  0.01
Respiratory Toxicity:  0.987

Download Data

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

  Natural Product: NPC474348

Natural Product ID:  NPC474348
Common Name*:   Dehydrodaphnigraciline
IUPAC Name:   n.a.
Synonyms:   Dehydrodaphnigraciline
Standard InCHIKey:  ONAGOPFNNJDPCW-XIQGKOAISA-N
Standard InCHI:  InChI=1S/C23H33NO3/c1-4-17-9-10-22(14-27-17)16-7-5-15-6-8-18-19(21(25)26-3)11-23(22,20(15)18)13-24(2)12-16/h9,16,18-19H,4-8,10-14H2,1-3H3/t16-,18-,19-,22+,23+/m1/s1
SMILES:  CCC1=CCC2(CO1)C3CCC4=C5C2(CC(C5CC4)C(=O)OC)CN(C3)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL465534
PubChem CID:   44567623
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000130] Azaspirodecane 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
NPO32797 daphniphyllum oldhami Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. PMID[18288811]
NPO32797 daphniphyllum oldhami Species Daphniphyllaceae Eukaryota n.a. n.a. n.a. PMID[19441852]

☑ 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
NPT20967 CELL-LINE Platelet n.a. Inhibition = 13.4 % PMID[484932]

☑ 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 NPC474348 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
0.93 High Similarity NPC470536
0.92 High Similarity NPC470535
0.8131 Intermediate Similarity NPC470531
0.8131 Intermediate Similarity NPC470528
0.8131 Intermediate Similarity NPC470529
0.8131 Intermediate Similarity NPC470532
0.8131 Intermediate Similarity NPC470533
0.8131 Intermediate Similarity NPC470527
0.8131 Intermediate Similarity NPC470530
0.8056 Intermediate Similarity NPC470534
0.7788 Intermediate Similarity NPC476952
0.7768 Intermediate Similarity NPC470538
0.7652 Intermediate Similarity NPC88190
0.7478 Intermediate Similarity NPC471109
0.7168 Intermediate Similarity NPC63511
0.7131 Intermediate Similarity NPC476951
0.7131 Intermediate Similarity NPC280903
0.7117 Intermediate Similarity NPC195841
0.7117 Intermediate Similarity NPC233256
0.7016 Intermediate Similarity NPC470539
0.6992 Remote Similarity NPC470537
0.6964 Remote Similarity NPC86906
0.6875 Remote Similarity NPC119329
0.6818 Remote Similarity NPC128698
0.6818 Remote Similarity NPC239768
0.6765 Remote Similarity NPC100391
0.6726 Remote Similarity NPC212874
0.6724 Remote Similarity NPC473232
0.6699 Remote Similarity NPC470223
0.6667 Remote Similarity NPC79238
0.6639 Remote Similarity NPC135431
0.6639 Remote Similarity NPC470540
0.6637 Remote Similarity NPC265094
0.6583 Remote Similarity NPC209252
0.6579 Remote Similarity NPC475239
0.6579 Remote Similarity NPC133420
0.6571 Remote Similarity NPC167877
0.6542 Remote Similarity NPC44240
0.6509 Remote Similarity NPC28227
0.6486 Remote Similarity NPC476344
0.6476 Remote Similarity NPC264127
0.6466 Remote Similarity NPC271562
0.6455 Remote Similarity NPC150041
0.6449 Remote Similarity NPC474679
0.6423 Remote Similarity NPC35037
0.6408 Remote Similarity NPC240302
0.6406 Remote Similarity NPC478136
0.64 Remote Similarity NPC15975
0.64 Remote Similarity NPC195785
0.6396 Remote Similarity NPC476449
0.6381 Remote Similarity NPC75810
0.6373 Remote Similarity NPC170038
0.6355 Remote Similarity NPC472220
0.6355 Remote Similarity NPC97884
0.6354 Remote Similarity NPC22301
0.6341 Remote Similarity NPC96731
0.633 Remote Similarity NPC218301
0.6327 Remote Similarity NPC107783
0.6327 Remote Similarity NPC470237
0.6327 Remote Similarity NPC92909
0.6325 Remote Similarity NPC46981
0.6321 Remote Similarity NPC195640
0.6311 Remote Similarity NPC255580
0.6311 Remote Similarity NPC39411
0.6303 Remote Similarity NPC472313
0.6296 Remote Similarity NPC474570
0.6293 Remote Similarity NPC87919
0.6286 Remote Similarity NPC165064
0.6286 Remote Similarity NPC109512
0.6286 Remote Similarity NPC475100
0.6275 Remote Similarity NPC469690
0.6275 Remote Similarity NPC477371
0.6275 Remote Similarity NPC182550
0.6275 Remote Similarity NPC118987
0.6273 Remote Similarity NPC93027
0.6273 Remote Similarity NPC470224
0.625 Remote Similarity NPC296367
0.625 Remote Similarity NPC474459
0.6239 Remote Similarity NPC471896
0.6239 Remote Similarity NPC175628
0.6239 Remote Similarity NPC148414
0.6239 Remote Similarity NPC111585
0.6228 Remote Similarity NPC477964
0.6226 Remote Similarity NPC323765
0.6226 Remote Similarity NPC283733
0.6218 Remote Similarity NPC147835
0.6218 Remote Similarity NPC253645
0.6218 Remote Similarity NPC85001
0.6218 Remote Similarity NPC95920
0.6216 Remote Similarity NPC124207
0.6214 Remote Similarity NPC276356
0.621 Remote Similarity NPC174463
0.6204 Remote Similarity NPC294480
0.6202 Remote Similarity NPC96010
0.6202 Remote Similarity NPC317654
0.62 Remote Similarity NPC469678
0.62 Remote Similarity NPC475771
0.62 Remote Similarity NPC469669
0.62 Remote Similarity NPC324762
0.6198 Remote Similarity NPC474452
0.6195 Remote Similarity NPC202705
0.6195 Remote Similarity NPC241426
0.619 Remote Similarity NPC470277
0.619 Remote Similarity NPC167103
0.619 Remote Similarity NPC108045
0.619 Remote Similarity NPC475622
0.6186 Remote Similarity NPC176773
0.6186 Remote Similarity NPC296522
0.6186 Remote Similarity NPC144511
0.6182 Remote Similarity NPC26888
0.6182 Remote Similarity NPC190442
0.6176 Remote Similarity NPC4827
0.6176 Remote Similarity NPC35574
0.6168 Remote Similarity NPC470050
0.6168 Remote Similarity NPC155011
0.6168 Remote Similarity NPC470051
0.6167 Remote Similarity NPC158854
0.6161 Remote Similarity NPC33473
0.6154 Remote Similarity NPC201912
0.6154 Remote Similarity NPC327002
0.6154 Remote Similarity NPC477372
0.6154 Remote Similarity NPC476988
0.6154 Remote Similarity NPC38350
0.6154 Remote Similarity NPC147066
0.6148 Remote Similarity NPC478137
0.6147 Remote Similarity NPC474889
0.6147 Remote Similarity NPC50070
0.614 Remote Similarity NPC91604
0.6139 Remote Similarity NPC476317
0.6139 Remote Similarity NPC226242
0.6132 Remote Similarity NPC238197
0.6132 Remote Similarity NPC194937
0.6132 Remote Similarity NPC476038
0.6126 Remote Similarity NPC229976
0.6122 Remote Similarity NPC472955
0.6117 Remote Similarity NPC274996
0.6117 Remote Similarity NPC216090
0.6117 Remote Similarity NPC327674
0.6117 Remote Similarity NPC170561
0.6117 Remote Similarity NPC153987
0.6117 Remote Similarity NPC469620
0.6117 Remote Similarity NPC158846
0.6117 Remote Similarity NPC471475
0.6117 Remote Similarity NPC44083
0.6117 Remote Similarity NPC196827
0.6116 Remote Similarity NPC58281
0.6111 Remote Similarity NPC128644
0.6111 Remote Similarity NPC478144
0.6111 Remote Similarity NPC96496
0.6111 Remote Similarity NPC142361
0.6111 Remote Similarity NPC159046
0.6111 Remote Similarity NPC230849
0.6111 Remote Similarity NPC11379
0.6111 Remote Similarity NPC233836
0.6111 Remote Similarity NPC478145
0.6111 Remote Similarity NPC312215
0.6111 Remote Similarity NPC474684
0.6111 Remote Similarity NPC187376
0.6106 Remote Similarity NPC322063
0.6106 Remote Similarity NPC307164
0.6106 Remote Similarity NPC58052
0.6106 Remote Similarity NPC111684
0.61 Remote Similarity NPC469691
0.61 Remote Similarity NPC167049
0.61 Remote Similarity NPC469643
0.61 Remote Similarity NPC166797
0.61 Remote Similarity NPC469641
0.61 Remote Similarity NPC472966
0.61 Remote Similarity NPC306928
0.6095 Remote Similarity NPC100297
0.6095 Remote Similarity NPC260956
0.6095 Remote Similarity NPC133391
0.6095 Remote Similarity NPC142683
0.6095 Remote Similarity NPC327969
0.6095 Remote Similarity NPC321289
0.6091 Remote Similarity NPC474842
0.6091 Remote Similarity NPC123854
0.6091 Remote Similarity NPC472866
0.6091 Remote Similarity NPC475965
0.6087 Remote Similarity NPC477521
0.608 Remote Similarity NPC470276
0.6078 Remote Similarity NPC476264
0.6078 Remote Similarity NPC476325
0.6075 Remote Similarity NPC78089
0.6071 Remote Similarity NPC56525
0.6071 Remote Similarity NPC159410
0.6068 Remote Similarity NPC97336
0.6066 Remote Similarity NPC80834
0.6066 Remote Similarity NPC469466
0.6066 Remote Similarity NPC469968
0.6063 Remote Similarity NPC476504
0.6063 Remote Similarity NPC238323
0.6058 Remote Similarity NPC302426
0.6058 Remote Similarity NPC47747
0.6055 Remote Similarity NPC472870
0.6055 Remote Similarity NPC183546
0.6055 Remote Similarity NPC247406
0.6055 Remote Similarity NPC48866
0.6055 Remote Similarity NPC203170
0.6053 Remote Similarity NPC475894

  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 NPC474348 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
0.717 Intermediate Similarity NPD5349 Clinical (unspecified phase)
0.6613 Remote Similarity NPD7122 Discontinued
0.6522 Remote Similarity NPD7333 Discontinued
0.6471 Remote Similarity NPD857 Phase 3
0.6355 Remote Similarity NPD6672 Approved
0.6355 Remote Similarity NPD5737 Approved
0.6355 Remote Similarity NPD6903 Approved
0.6321 Remote Similarity NPD7521 Approved
0.6321 Remote Similarity NPD7334 Approved
0.6321 Remote Similarity NPD7146 Approved
0.6321 Remote Similarity NPD5330 Approved
0.6321 Remote Similarity NPD6409 Approved
0.6321 Remote Similarity NPD6684 Approved
0.6204 Remote Similarity NPD7513 Clinical (unspecified phase)
0.6179 Remote Similarity NPD4766 Approved
0.6168 Remote Similarity NPD6098 Approved
0.6167 Remote Similarity NPD1752 Approved
0.6167 Remote Similarity NPD1756 Approved
0.616 Remote Similarity NPD7517 Approved
0.616 Remote Similarity NPD7519 Approved
0.616 Remote Similarity NPD7518 Approved
0.6154 Remote Similarity NPD8336 Approved
0.6154 Remote Similarity NPD8337 Approved
0.6126 Remote Similarity NPD6399 Phase 3
0.6063 Remote Similarity NPD6909 Approved
0.6063 Remote Similarity NPD6908 Approved
0.6038 Remote Similarity NPD5362 Discontinued
0.602 Remote Similarity NPD3726 Approved
0.602 Remote Similarity NPD3725 Approved
0.6018 Remote Similarity NPD6356 Clinical (unspecified phase)
0.6 Remote Similarity NPD6080 Approved
0.6 Remote Similarity NPD6673 Approved
0.6 Remote Similarity NPD6904 Approved
0.5982 Remote Similarity NPD5781 Clinical (unspecified phase)
0.597 Remote Similarity NPD8338 Approved
0.5952 Remote Similarity NPD4574 Approved
0.5952 Remote Similarity NPD4576 Approved
0.5946 Remote Similarity NPD5207 Approved
0.5943 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5913 Remote Similarity NPD6084 Phase 2
0.5913 Remote Similarity NPD6083 Phase 2
0.5909 Remote Similarity NPD5208 Approved
0.5906 Remote Similarity NPD2117 Pre-registration
0.5906 Remote Similarity NPD2116 Approved
0.5906 Remote Similarity NPD2115 Approved
0.5902 Remote Similarity NPD6420 Discontinued
0.5893 Remote Similarity NPD6050 Approved
0.5888 Remote Similarity NPD7154 Phase 3
0.5877 Remote Similarity NPD5695 Phase 3
0.5865 Remote Similarity NPD5784 Clinical (unspecified phase)
0.5859 Remote Similarity NPD2695 Approved
0.5859 Remote Similarity NPD2696 Approved
0.5859 Remote Similarity NPD2694 Approved
0.5859 Remote Similarity NPD2697 Approved
0.5859 Remote Similarity NPD2994 Approved
0.5852 Remote Similarity NPD6845 Suspended
0.5833 Remote Similarity NPD4786 Approved
0.5814 Remote Similarity NPD3031 Approved
0.5814 Remote Similarity NPD3030 Approved
0.5814 Remote Similarity NPD3032 Approved
0.5806 Remote Similarity NPD7335 Phase 2
0.5806 Remote Similarity NPD7337 Clinical (unspecified phase)
0.5806 Remote Similarity NPD7336 Phase 2
0.5806 Remote Similarity NPD8077 Approved
0.5806 Remote Similarity NPD8078 Approved
0.5804 Remote Similarity NPD5692 Phase 3
0.5802 Remote Similarity NPD7437 Approved
0.5802 Remote Similarity NPD7436 Approved
0.5789 Remote Similarity NPD6001 Approved
0.5778 Remote Similarity NPD7260 Phase 2
0.5752 Remote Similarity NPD5693 Phase 1
0.5752 Remote Similarity NPD5694 Approved
0.5752 Remote Similarity NPD6411 Approved
0.5748 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5728 Remote Similarity NPD8039 Approved
0.5726 Remote Similarity NPD5696 Approved
0.5725 Remote Similarity NPD2946 Phase 2
0.5714 Remote Similarity NPD1695 Approved
0.5682 Remote Similarity NPD4217 Approved
0.5682 Remote Similarity NPD3131 Approved
0.5682 Remote Similarity NPD4216 Approved
0.5682 Remote Similarity NPD3132 Approved
0.5682 Remote Similarity NPD2612 Approved
0.5682 Remote Similarity NPD2610 Approved
0.5682 Remote Similarity NPD2608 Approved
0.5682 Remote Similarity NPD2611 Approved
0.5682 Remote Similarity NPD4215 Approved
0.5682 Remote Similarity NPD2609 Approved
0.5682 Remote Similarity NPD4218 Approved
0.568 Remote Similarity NPD6053 Discontinued
0.5678 Remote Similarity NPD6404 Discontinued
0.5669 Remote Similarity NPD7754 Approved
0.5669 Remote Similarity NPD7755 Approved
0.5652 Remote Similarity NPD5282 Discontinued
0.5648 Remote Similarity NPD3667 Approved
0.5648 Remote Similarity NPD6435 Approved
0.5645 Remote Similarity NPD4234 Approved
0.5645 Remote Similarity NPD4233 Approved
0.5645 Remote Similarity NPD3646 Clinical (unspecified phase)
0.5639 Remote Similarity NPD8273 Phase 1
0.5636 Remote Similarity NPD7520 Clinical (unspecified phase)
0.5636 Remote Similarity NPD1694 Approved
0.5635 Remote Similarity NPD2607 Approved
0.5614 Remote Similarity NPD8034 Phase 2
0.5614 Remote Similarity NPD8035 Phase 2
0.561 Remote Similarity NPD7320 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