Structure

Physi-Chem Properties

Molecular Weight:  277.17
Volume:  283.161
LogP:  1.04
LogD:  0.833
LogS:  -1.41
# Rotatable Bonds:  0
TPSA:  49.77
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  4
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.726
Synthetic Accessibility Score:  4.797
Fsp3:  0.812
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.765
MDCK Permeability:  6.509192462544888e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.52
Human Intestinal Absorption (HIA):  0.434
20% Bioavailability (F20%):  0.03
30% Bioavailability (F30%):  0.877

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.98
Plasma Protein Binding (PPB):  33.65421676635742%
Volume Distribution (VD):  4.784
Pgp-substrate:  66.80225372314453%

ADMET: Metabolism

CYP1A2-inhibitor:  0.031
CYP1A2-substrate:  0.109
CYP2C19-inhibitor:  0.026
CYP2C19-substrate:  0.891
CYP2C9-inhibitor:  0.006
CYP2C9-substrate:  0.073
CYP2D6-inhibitor:  0.036
CYP2D6-substrate:  0.624
CYP3A4-inhibitor:  0.069
CYP3A4-substrate:  0.468

ADMET: Excretion

Clearance (CL):  17.119
Half-life (T1/2):  0.733

ADMET: Toxicity

hERG Blockers:  0.079
Human Hepatotoxicity (H-HT):  0.366
Drug-inuced Liver Injury (DILI):  0.189
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.872
Maximum Recommended Daily Dose:  0.881
Skin Sensitization:  0.524
Carcinogencity:  0.839
Eye Corrosion:  0.735
Eye Irritation:  0.222
Respiratory Toxicity:  0.962

Download Data

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

  Natural Product: NPC176773

Natural Product ID:  NPC176773
Common Name*:   Grandisine C
IUPAC Name:   (6aR,9S,11S,12aS,12bS)-9-hydroxy-11-methyl-1,2,3,5,6,6a,8,9,10,11,12a,12b-dodecahydrochromeno[2,3-g]indolizin-12-one
Synonyms:   Grandisine C
Standard InCHIKey:  WNDBXOYUMYCREE-NAYUARGSSA-N
Standard InCHI:  InChI=1S/C16H23NO3/c1-9-7-10(18)8-13-14(9)16(19)15-11-3-2-5-17(11)6-4-12(15)20-13/h9-12,15,18H,2-8H2,1H3/t9-,10-,11-,12+,15-/m0/s1
SMILES:  O[C@H]1C[C@H](C)C2=C(C1)O[C@H]1[C@@H](C2=O)[C@@H]2CCCN2CC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL509995
PubChem CID:   16086540
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000251] Indolizidines

*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
NPO9570 Elaeocarpus grandis Species Elaeocarpaceae Eukaryota n.a. Australian rainforest n.a. PMID[16989522]

☑ 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
NPT271 Individual Protein Delta opioid receptor Homo sapiens IC50 = 14600.0 nM PMID[506196]

☑ 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 NPC176773 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
0.8302 Intermediate Similarity NPC87919
0.7963 Intermediate Similarity NPC133420
0.687 Remote Similarity NPC475239
0.678 Remote Similarity NPC274895
0.6774 Remote Similarity NPC13351
0.6762 Remote Similarity NPC277918
0.6697 Remote Similarity NPC469464
0.6667 Remote Similarity NPC475987
0.6667 Remote Similarity NPC313348
0.664 Remote Similarity NPC477143
0.664 Remote Similarity NPC477140
0.6609 Remote Similarity NPC181645
0.6589 Remote Similarity NPC96010
0.6589 Remote Similarity NPC317654
0.6583 Remote Similarity NPC473232
0.6574 Remote Similarity NPC473525
0.6565 Remote Similarity NPC478139
0.6491 Remote Similarity NPC20078
0.6491 Remote Similarity NPC473574
0.6481 Remote Similarity NPC322672
0.648 Remote Similarity NPC96731
0.6475 Remote Similarity NPC261750
0.6475 Remote Similarity NPC1111
0.6423 Remote Similarity NPC473955
0.6417 Remote Similarity NPC476276
0.6417 Remote Similarity NPC470535
0.6389 Remote Similarity NPC76283
0.6389 Remote Similarity NPC319913
0.6364 Remote Similarity NPC470536
0.6364 Remote Similarity NPC143025
0.6349 Remote Similarity NPC476952
0.6348 Remote Similarity NPC472166
0.6341 Remote Similarity NPC60432
0.633 Remote Similarity NPC472161
0.633 Remote Similarity NPC472136
0.6325 Remote Similarity NPC77703
0.632 Remote Similarity NPC30196
0.6308 Remote Similarity NPC317474
0.6308 Remote Similarity NPC291027
0.6308 Remote Similarity NPC169485
0.6308 Remote Similarity NPC213126
0.6308 Remote Similarity NPC84281
0.6293 Remote Similarity NPC91604
0.629 Remote Similarity NPC477963
0.627 Remote Similarity NPC6531
0.626 Remote Similarity NPC470534
0.626 Remote Similarity NPC309525
0.625 Remote Similarity NPC476328
0.624 Remote Similarity NPC145501
0.6231 Remote Similarity NPC314629
0.623 Remote Similarity NPC474725
0.622 Remote Similarity NPC474006
0.622 Remote Similarity NPC471673
0.6216 Remote Similarity NPC116231
0.6212 Remote Similarity NPC470537
0.6212 Remote Similarity NPC280903
0.6207 Remote Similarity NPC476344
0.6198 Remote Similarity NPC475800
0.619 Remote Similarity NPC178852
0.6186 Remote Similarity NPC474348
0.6179 Remote Similarity NPC478209
0.6176 Remote Similarity NPC120420
0.6174 Remote Similarity NPC150041
0.6167 Remote Similarity NPC212874
0.6161 Remote Similarity NPC97577
0.6154 Remote Similarity NPC35717
0.6154 Remote Similarity NPC306908
0.6134 Remote Similarity NPC163249
0.6134 Remote Similarity NPC473289
0.6134 Remote Similarity NPC476755
0.6132 Remote Similarity NPC475681
0.6131 Remote Similarity NPC99864
0.6126 Remote Similarity NPC324506
0.6124 Remote Similarity NPC11379
0.6124 Remote Similarity NPC88190
0.6121 Remote Similarity NPC472734
0.6121 Remote Similarity NPC472733
0.6121 Remote Similarity NPC476449
0.6121 Remote Similarity NPC289140
0.6119 Remote Similarity NPC316205
0.6119 Remote Similarity NPC315387
0.6116 Remote Similarity NPC86906
0.6116 Remote Similarity NPC471333
0.6116 Remote Similarity NPC471332
0.6111 Remote Similarity NPC135431
0.6111 Remote Similarity NPC473810
0.6106 Remote Similarity NPC312637
0.6098 Remote Similarity NPC218602
0.6094 Remote Similarity NPC201889
0.6094 Remote Similarity NPC471109
0.6094 Remote Similarity NPC106791
0.6091 Remote Similarity NPC478245
0.609 Remote Similarity NPC476951
0.6083 Remote Similarity NPC474563
0.6083 Remote Similarity NPC265094
0.6083 Remote Similarity NPC98765
0.6077 Remote Similarity NPC23963
0.6077 Remote Similarity NPC238323
0.6071 Remote Similarity NPC53911
0.6071 Remote Similarity NPC185059
0.6071 Remote Similarity NPC53454
0.6071 Remote Similarity NPC475001
0.6068 Remote Similarity NPC27105
0.6068 Remote Similarity NPC472732
0.6068 Remote Similarity NPC472167
0.6068 Remote Similarity NPC472731
0.6068 Remote Similarity NPC472162
0.6066 Remote Similarity NPC46981
0.6066 Remote Similarity NPC271562
0.6063 Remote Similarity NPC470538
0.6063 Remote Similarity NPC209252
0.6055 Remote Similarity NPC107498
0.6055 Remote Similarity NPC185949
0.6053 Remote Similarity NPC248913
0.6053 Remote Similarity NPC36491
0.6048 Remote Similarity NPC476290
0.6047 Remote Similarity NPC35037
0.6045 Remote Similarity NPC471086
0.6045 Remote Similarity NPC478136
0.6034 Remote Similarity NPC25033
0.6034 Remote Similarity NPC476261
0.6034 Remote Similarity NPC91408
0.6034 Remote Similarity NPC279313
0.6034 Remote Similarity NPC119225
0.6034 Remote Similarity NPC470382
0.6034 Remote Similarity NPC471635
0.6032 Remote Similarity NPC478212
0.6029 Remote Similarity NPC261730
0.6029 Remote Similarity NPC120335
0.6019 Remote Similarity NPC14151
0.6017 Remote Similarity NPC472729
0.6017 Remote Similarity NPC472687
0.6017 Remote Similarity NPC177680
0.6017 Remote Similarity NPC99657
0.6017 Remote Similarity NPC203388
0.6017 Remote Similarity NPC472730
0.6017 Remote Similarity NPC471331
0.6017 Remote Similarity NPC153776
0.6017 Remote Similarity NPC471330
0.6016 Remote Similarity NPC140251
0.6016 Remote Similarity NPC307903
0.6 Remote Similarity NPC477436
0.6 Remote Similarity NPC21713
0.6 Remote Similarity NPC477435
0.6 Remote Similarity NPC475608
0.5985 Remote Similarity NPC69496
0.5985 Remote Similarity NPC318445
0.5985 Remote Similarity NPC316133
0.5984 Remote Similarity NPC143268
0.5984 Remote Similarity NPC45218
0.5984 Remote Similarity NPC323821
0.5984 Remote Similarity NPC247069
0.5984 Remote Similarity NPC268238
0.5982 Remote Similarity NPC272039
0.5982 Remote Similarity NPC38885
0.5982 Remote Similarity NPC197333
0.5982 Remote Similarity NPC220930
0.5982 Remote Similarity NPC298904
0.598 Remote Similarity NPC477455
0.5972 Remote Similarity NPC276822
0.5969 Remote Similarity NPC156336
0.5969 Remote Similarity NPC120599
0.5969 Remote Similarity NPC200412
0.5968 Remote Similarity NPC470615
0.5968 Remote Similarity NPC20192
0.5968 Remote Similarity NPC473578
0.5966 Remote Similarity NPC472727
0.5966 Remote Similarity NPC476299
0.5966 Remote Similarity NPC474012
0.5966 Remote Similarity NPC472728
0.5965 Remote Similarity NPC113393
0.5965 Remote Similarity NPC230332
0.5965 Remote Similarity NPC478258
0.5965 Remote Similarity NPC478257
0.5956 Remote Similarity NPC215507
0.5952 Remote Similarity NPC314550
0.5952 Remote Similarity NPC476269
0.595 Remote Similarity NPC320294
0.5948 Remote Similarity NPC114162
0.5948 Remote Similarity NPC212812
0.5948 Remote Similarity NPC469819
0.5946 Remote Similarity NPC68303
0.5946 Remote Similarity NPC307126
0.5946 Remote Similarity NPC197823
0.5946 Remote Similarity NPC92633
0.5941 Remote Similarity NPC477452
0.594 Remote Similarity NPC471087
0.594 Remote Similarity NPC326386
0.594 Remote Similarity NPC477985
0.5938 Remote Similarity NPC288629
0.5938 Remote Similarity NPC173686
0.5938 Remote Similarity NPC16081
0.5935 Remote Similarity NPC202524
0.5933 Remote Similarity NPC475342
0.5932 Remote Similarity NPC140300
0.5932 Remote Similarity NPC474164
0.5932 Remote Similarity NPC478233
0.5929 Remote Similarity NPC307298
0.5929 Remote Similarity NPC328539
0.5929 Remote Similarity NPC131470

  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 NPC176773 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
0.6803 Remote Similarity NPD8137 Clinical (unspecified phase)
0.68 Remote Similarity NPD8080 Discontinued
0.672 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6549 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6308 Remote Similarity NPD3132 Approved
0.6308 Remote Similarity NPD3131 Approved
0.6308 Remote Similarity NPD2611 Approved
0.6308 Remote Similarity NPD4218 Approved
0.6308 Remote Similarity NPD4216 Approved
0.6308 Remote Similarity NPD2608 Approved
0.6308 Remote Similarity NPD4215 Approved
0.6308 Remote Similarity NPD2609 Approved
0.6308 Remote Similarity NPD4217 Approved
0.6308 Remote Similarity NPD2612 Approved
0.6308 Remote Similarity NPD2610 Approved
0.625 Remote Similarity NPD7333 Discontinued
0.6172 Remote Similarity NPD7517 Approved
0.6172 Remote Similarity NPD7519 Approved
0.6172 Remote Similarity NPD7518 Approved
0.6161 Remote Similarity NPD6101 Approved
0.6161 Remote Similarity NPD5764 Clinical (unspecified phase)
0.616 Remote Similarity NPD1376 Discontinued
0.6154 Remote Similarity NPD2838 Clinical (unspecified phase)
0.6131 Remote Similarity NPD8415 Approved
0.6103 Remote Similarity NPD6845 Suspended
0.6094 Remote Similarity NPD7641 Discontinued
0.6087 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6077 Remote Similarity NPD6908 Approved
0.6077 Remote Similarity NPD6909 Approved
0.6053 Remote Similarity NPD6411 Approved
0.5985 Remote Similarity NPD2613 Approved
0.5985 Remote Similarity NPD7642 Approved
0.5948 Remote Similarity NPD5282 Discontinued
0.5882 Remote Similarity NPD2694 Approved
0.5882 Remote Similarity NPD2697 Approved
0.5882 Remote Similarity NPD2695 Approved
0.5882 Remote Similarity NPD2696 Approved
0.5877 Remote Similarity NPD5328 Approved
0.5857 Remote Similarity NPD3615 Approved
0.5857 Remote Similarity NPD2566 Approved
0.5857 Remote Similarity NPD4745 Approved
0.5857 Remote Similarity NPD3614 Approved
0.5857 Remote Similarity NPD2574 Discontinued
0.5857 Remote Similarity NPD2570 Approved
0.5857 Remote Similarity NPD2573 Approved
0.5857 Remote Similarity NPD3616 Approved
0.5857 Remote Similarity NPD3090 Approved
0.5857 Remote Similarity NPD2572 Clinical (unspecified phase)
0.5857 Remote Similarity NPD3089 Approved
0.5857 Remote Similarity NPD2571 Approved
0.5857 Remote Similarity NPD3088 Approved
0.5857 Remote Similarity NPD4746 Phase 3
0.5857 Remote Similarity NPD3087 Approved
0.5854 Remote Similarity NPD6920 Discontinued
0.5839 Remote Similarity NPD6914 Discontinued
0.5833 Remote Similarity NPD6921 Approved
0.5821 Remote Similarity NPD8342 Approved
0.5821 Remote Similarity NPD8340 Approved
0.5821 Remote Similarity NPD8299 Approved
0.5821 Remote Similarity NPD8341 Approved
0.5818 Remote Similarity NPD3667 Approved
0.5809 Remote Similarity NPD8336 Approved
0.5809 Remote Similarity NPD8337 Approved
0.5802 Remote Similarity NPD2132 Phase 3
0.58 Remote Similarity NPD7341 Phase 2
0.5778 Remote Similarity NPD8273 Phase 1
0.5778 Remote Similarity NPD8451 Approved
0.5776 Remote Similarity NPD6079 Approved
0.5775 Remote Similarity NPD4686 Approved
0.5775 Remote Similarity NPD4684 Phase 3
0.5775 Remote Similarity NPD4685 Phase 3
0.5764 Remote Similarity NPD8384 Approved
0.5755 Remote Similarity NPD8338 Approved
0.5752 Remote Similarity NPD3618 Phase 1
0.5738 Remote Similarity NPD8085 Approved
0.5738 Remote Similarity NPD8083 Approved
0.5738 Remote Similarity NPD8086 Approved
0.5738 Remote Similarity NPD8084 Approved
0.5738 Remote Similarity NPD8082 Approved
0.5738 Remote Similarity NPD8138 Approved
0.5738 Remote Similarity NPD8139 Approved
0.5735 Remote Similarity NPD5157 Phase 1
0.5735 Remote Similarity NPD5158 Clinical (unspecified phase)
0.5735 Remote Similarity NPD5159 Phase 2
0.5735 Remote Similarity NPD8448 Approved
0.5726 Remote Similarity NPD5778 Approved
0.5726 Remote Similarity NPD5779 Approved
0.5725 Remote Similarity NPD8391 Approved
0.5725 Remote Similarity NPD8392 Approved
0.5725 Remote Similarity NPD8390 Approved
0.5714 Remote Similarity NPD4786 Approved
0.5714 Remote Similarity NPD3665 Phase 1
0.5714 Remote Similarity NPD3133 Approved
0.5714 Remote Similarity NPD3666 Approved
0.5694 Remote Similarity NPD2567 Approved
0.5694 Remote Similarity NPD2569 Approved
0.5692 Remote Similarity NPD1711 Phase 2
0.5691 Remote Similarity NPD8276 Approved
0.5691 Remote Similarity NPD8275 Approved
0.5683 Remote Similarity NPD2101 Approved
0.5683 Remote Similarity NPD7260 Phase 2
0.568 Remote Similarity NPD8140 Approved
0.5667 Remote Similarity NPD4755 Approved
0.5645 Remote Similarity NPD8081 Approved
0.5639 Remote Similarity NPD1689 Approved
0.5635 Remote Similarity NPD6415 Discontinued
0.563 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5625 Remote Similarity NPD2204 Approved
0.5615 Remote Similarity NPD1000 Clinical (unspecified phase)
0.5614 Remote Similarity NPD5279 Phase 3
0.56 Remote Similarity NPD7128 Approved
0.56 Remote Similarity NPD5739 Approved
0.56 Remote Similarity NPD8393 Approved
0.56 Remote Similarity NPD6402 Approved
0.56 Remote Similarity NPD6675 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