Structure

Physi-Chem Properties

Molecular Weight:  1182.57
Volume:  1103.051
LogP:  -0.439
LogD:  0.5
LogS:  -2.499
# Rotatable Bonds:  13
TPSA:  414.21
# H-Bond Aceptor:  27
# H-Bond Donor:  15
# Rings:  11
# Heavy Atoms:  27

MedChem Properties

QED Drug-Likeness Score:  0.077
Synthetic Accessibility Score:  7.661
Fsp3:  1.0
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.386
MDCK Permeability:  0.000696191331371665
Pgp-inhibitor:  0.0
Pgp-substrate:  1.0
Human Intestinal Absorption (HIA):  1.0
20% Bioavailability (F20%):  0.122
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.185
Plasma Protein Binding (PPB):  39.76774215698242%
Volume Distribution (VD):  -0.333
Pgp-substrate:  20.039657592773438%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.046
CYP2C19-inhibitor:  0.001
CYP2C19-substrate:  0.05
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.0
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.037
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.001

ADMET: Excretion

Clearance (CL):  -0.097
Half-life (T1/2):  0.773

ADMET: Toxicity

hERG Blockers:  0.921
Human Hepatotoxicity (H-HT):  0.135
Drug-inuced Liver Injury (DILI):  0.103
AMES Toxicity:  0.075
Rat Oral Acute Toxicity:  0.067
Maximum Recommended Daily Dose:  0.004
Skin Sensitization:  0.967
Carcinogencity:  0.08
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.923

Download Data

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

  Natural Product: NPC476112

Natural Product ID:  NPC476112
Common Name*:   LJRKVIYLPKSCPE-MXEBQRMESA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LJRKVIYLPKSCPE-MXEBQRMESA-N
Standard InCHI:  InChI=1S/C55H90O27/c1-20-5-10-55(73-17-20)21(2)34-30(82-55)13-25-23-12-27(59)26-11-22(6-8-53(26,3)24(23)7-9-54(25,34)4)74-50-42(69)39(66)44(33(16-58)77-50)78-52-47(46(38(65)32(15-57)76-52)80-49-41(68)36(63)29(61)19-72-49)81-51-43(70)45(37(64)31(14-56)75-51)79-48-40(67)35(62)28(60)18-71-48/h20-52,56-70H,5-19H2,1-4H3/t20?,21-,22-,23+,24-,25-,26+,27-,28+,29+,30-,31+,32+,33+,34-,35-,36-,37+,38+,39+,40+,41+,42+,43+,44-,45-,46-,47+,48-,49-,50+,51-,52-,53+,54-,55+/m0/s1
SMILES:  CC1CCC2(C(C3C(O2)CC4C3(CCC5C4CC(C6C5(CCC(C6)OC7C(C(C(C(O7)CO)OC8C(C(C(C(O8)CO)O)OC9C(C(C(CO9)O)O)O)OC2C(C(C(C(O2)CO)O)OC2C(C(C(CO2)O)O)O)O)O)O)C)O)C)C)OC1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL527055
PubChem CID:   44558940
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000258] Steroids and steroid derivatives
        • [CHEMONTID:0001013] Steroidal glycosides
          • [CHEMONTID:0002364] Steroidal saponins

*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
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota aerial parts n.a. n.a. PMID[11087596]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota underground parts n.a. n.a. PMID[12398537]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota fresh tubers n.a. n.a. PMID[14738376]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO12929 Polianthes tuberosa Species Asparagaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO12929 Polianthes tuberosa Species Asparagaceae 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
NPT116 Cell Line HL-60 Homo sapiens IC50 = 2.6 ug.mL-1 PMID[508790]

☑ 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 NPC476112 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
1.0 High Similarity NPC307534
0.989 High Similarity NPC473518
0.9889 High Similarity NPC132080
0.9889 High Similarity NPC128572
0.9889 High Similarity NPC184617
0.9889 High Similarity NPC84111
0.9889 High Similarity NPC30856
0.9889 High Similarity NPC287483
0.9889 High Similarity NPC284104
0.9889 High Similarity NPC475643
0.9889 High Similarity NPC475625
0.9889 High Similarity NPC470864
0.9889 High Similarity NPC232037
0.9889 High Similarity NPC97700
0.9889 High Similarity NPC160426
0.9889 High Similarity NPC98018
0.9889 High Similarity NPC470865
0.9889 High Similarity NPC470866
0.9889 High Similarity NPC103616
0.9889 High Similarity NPC116756
0.9889 High Similarity NPC470863
0.978 High Similarity NPC83137
0.978 High Similarity NPC470861
0.978 High Similarity NPC232611
0.978 High Similarity NPC470862
0.978 High Similarity NPC51520
0.978 High Similarity NPC115165
0.978 High Similarity NPC303069
0.9778 High Similarity NPC473727
0.9778 High Similarity NPC211354
0.9778 High Similarity NPC6295
0.9778 High Similarity NPC107962
0.9778 High Similarity NPC107188
0.9778 High Similarity NPC473610
0.9778 High Similarity NPC475351
0.9778 High Similarity NPC19400
0.9778 High Similarity NPC206003
0.9674 High Similarity NPC291548
0.967 High Similarity NPC304011
0.967 High Similarity NPC195297
0.967 High Similarity NPC139271
0.967 High Similarity NPC121453
0.967 High Similarity NPC473601
0.9667 High Similarity NPC131693
0.9667 High Similarity NPC473851
0.9667 High Similarity NPC264101
0.9667 High Similarity NPC174024
0.9667 High Similarity NPC312678
0.9667 High Similarity NPC471464
0.9667 High Similarity NPC291547
0.9667 High Similarity NPC217205
0.9667 High Similarity NPC253268
0.9667 High Similarity NPC291203
0.9667 High Similarity NPC179859
0.9667 High Similarity NPC475436
0.9565 High Similarity NPC274200
0.9556 High Similarity NPC177834
0.9556 High Similarity NPC137004
0.9556 High Similarity NPC141769
0.9556 High Similarity NPC249204
0.9556 High Similarity NPC234352
0.9556 High Similarity NPC48339
0.9556 High Similarity NPC144790
0.9556 High Similarity NPC325828
0.9556 High Similarity NPC250393
0.9556 High Similarity NPC297348
0.9556 High Similarity NPC149400
0.9556 High Similarity NPC477451
0.9556 High Similarity NPC88962
0.9556 High Similarity NPC477547
0.9556 High Similarity NPC172838
0.9451 High Similarity NPC252253
0.9451 High Similarity NPC45959
0.9451 High Similarity NPC305418
0.9451 High Similarity NPC294686
0.9451 High Similarity NPC24960
0.9451 High Similarity NPC473774
0.9451 High Similarity NPC222731
0.9355 High Similarity NPC477222
0.9355 High Similarity NPC477223
0.9348 High Similarity NPC474399
0.9333 High Similarity NPC65550
0.9333 High Similarity NPC473542
0.9247 High Similarity NPC142264
0.9247 High Similarity NPC476510
0.9231 High Similarity NPC204881
0.9231 High Similarity NPC5632
0.9231 High Similarity NPC473830
0.9231 High Similarity NPC210759
0.9231 High Similarity NPC149966
0.9231 High Similarity NPC307167
0.9231 High Similarity NPC229801
0.9149 High Similarity NPC233649
0.9149 High Similarity NPC475207
0.9149 High Similarity NPC470028
0.9149 High Similarity NPC470591
0.913 High Similarity NPC311246
0.913 High Similarity NPC473726
0.913 High Similarity NPC167644
0.9111 High Similarity NPC281004
0.9062 High Similarity NPC475574
0.9053 High Similarity NPC473616
0.9032 High Similarity NPC3538
0.9032 High Similarity NPC477224
0.9032 High Similarity NPC175
0.9032 High Similarity NPC309866
0.9032 High Similarity NPC113500
0.9011 High Similarity NPC473472
0.9011 High Similarity NPC82955
0.9011 High Similarity NPC102725
0.9011 High Similarity NPC131466
0.9011 High Similarity NPC20822
0.8947 High Similarity NPC210157
0.8936 High Similarity NPC189575
0.8936 High Similarity NPC106701
0.8936 High Similarity NPC92196
0.8936 High Similarity NPC205129
0.8936 High Similarity NPC473064
0.8936 High Similarity NPC477494
0.8936 High Similarity NPC471425
0.8936 High Similarity NPC471429
0.8936 High Similarity NPC473065
0.8936 High Similarity NPC473067
0.8936 High Similarity NPC471424
0.8913 High Similarity NPC279329
0.8913 High Similarity NPC223143
0.8866 High Similarity NPC472081
0.8866 High Similarity NPC108227
0.8866 High Similarity NPC476512
0.8854 High Similarity NPC473638
0.8842 High Similarity NPC237071
0.8842 High Similarity NPC203434
0.8842 High Similarity NPC296936
0.8842 High Similarity NPC238796
0.883 High Similarity NPC77717
0.883 High Similarity NPC267238
0.883 High Similarity NPC471373
0.883 High Similarity NPC148593
0.883 High Similarity NPC253611
0.8817 High Similarity NPC473637
0.8817 High Similarity NPC476668
0.8817 High Similarity NPC36372
0.8817 High Similarity NPC293609
0.8812 High Similarity NPC473817
0.8812 High Similarity NPC220836
0.8812 High Similarity NPC94086
0.8812 High Similarity NPC92297
0.8812 High Similarity NPC233433
0.8812 High Similarity NPC273002
0.8791 High Similarity NPC43912
0.8791 High Similarity NPC140446
0.8776 High Similarity NPC470029
0.8776 High Similarity NPC310138
0.8776 High Similarity NPC134967
0.8776 High Similarity NPC114700
0.8725 High Similarity NPC470867
0.8723 High Similarity NPC277774
0.8723 High Similarity NPC224003
0.8723 High Similarity NPC18724
0.8723 High Similarity NPC323231
0.8723 High Similarity NPC470623
0.8723 High Similarity NPC476669
0.8723 High Similarity NPC171741
0.8713 High Similarity NPC125324
0.8713 High Similarity NPC92890
0.8713 High Similarity NPC49032
0.8713 High Similarity NPC51172
0.8713 High Similarity NPC475319
0.8713 High Similarity NPC202898
0.8687 High Similarity NPC476837
0.8687 High Similarity NPC139181
0.8687 High Similarity NPC97260
0.8673 High Similarity NPC476839
0.8673 High Similarity NPC477225
0.8673 High Similarity NPC476838
0.8632 High Similarity NPC473503
0.8632 High Similarity NPC475325
0.8632 High Similarity NPC30687
0.8627 High Similarity NPC151134
0.8617 High Similarity NPC59006
0.8586 High Similarity NPC310031
0.8586 High Similarity NPC80191
0.8571 High Similarity NPC290612
0.8571 High Similarity NPC471428
0.8571 High Similarity NPC471426
0.8571 High Similarity NPC471427
0.8571 High Similarity NPC273290
0.8571 High Similarity NPC232044
0.8542 High Similarity NPC57964
0.8542 High Similarity NPC94582
0.8542 High Similarity NPC469710
0.8515 High Similarity NPC215408
0.8469 Intermediate Similarity NPC471374
0.8469 Intermediate Similarity NPC471375
0.8469 Intermediate Similarity NPC209798
0.8462 Intermediate Similarity NPC227260
0.8462 Intermediate Similarity NPC92710
0.8454 Intermediate Similarity NPC473287
0.8444 Intermediate Similarity NPC296734
0.8444 Intermediate Similarity NPC470611

  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 NPC476112 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
0.9556 High Similarity NPD8171 Discontinued
0.86 High Similarity NPD8170 Clinical (unspecified phase)
0.8222 Intermediate Similarity NPD6928 Phase 2
0.7544 Intermediate Similarity NPD8294 Approved
0.7544 Intermediate Similarity NPD8377 Approved
0.7478 Intermediate Similarity NPD8335 Approved
0.7478 Intermediate Similarity NPD8296 Approved
0.7478 Intermediate Similarity NPD8380 Approved
0.7478 Intermediate Similarity NPD8379 Approved
0.7478 Intermediate Similarity NPD8378 Approved
0.7477 Intermediate Similarity NPD8133 Approved
0.7328 Intermediate Similarity NPD8033 Approved
0.7282 Intermediate Similarity NPD7991 Discontinued
0.7069 Intermediate Similarity NPD7327 Approved
0.7069 Intermediate Similarity NPD7328 Approved
0.7009 Intermediate Similarity NPD7516 Approved
0.6923 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6825 Remote Similarity NPD8450 Suspended
0.6809 Remote Similarity NPD1810 Approved
0.6809 Remote Similarity NPD1811 Approved
0.6746 Remote Similarity NPD8449 Approved
0.6667 Remote Similarity NPD8132 Clinical (unspecified phase)
0.6667 Remote Similarity NPD7507 Approved
0.6637 Remote Similarity NPD6412 Phase 2
0.6612 Remote Similarity NPD7503 Approved
0.6555 Remote Similarity NPD8295 Clinical (unspecified phase)
0.6508 Remote Similarity NPD7319 Approved
0.6489 Remote Similarity NPD2687 Approved
0.6489 Remote Similarity NPD2686 Approved
0.6489 Remote Similarity NPD2254 Approved
0.6471 Remote Similarity NPD6940 Discontinued
0.6435 Remote Similarity NPD8174 Phase 2
0.6429 Remote Similarity NPD7736 Approved
0.6373 Remote Similarity NPD3670 Clinical (unspecified phase)
0.6373 Remote Similarity NPD3669 Approved
0.6371 Remote Similarity NPD8328 Phase 3
0.6364 Remote Similarity NPD6118 Approved
0.6364 Remote Similarity NPD6115 Approved
0.6364 Remote Similarity NPD6114 Approved
0.6364 Remote Similarity NPD6697 Approved
0.6316 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6316 Remote Similarity NPD4787 Phase 1
0.629 Remote Similarity NPD6370 Approved
0.6263 Remote Similarity NPD6116 Phase 1
0.6222 Remote Similarity NPD6123 Approved
0.622 Remote Similarity NPD8293 Discontinued
0.6162 Remote Similarity NPD6117 Approved
0.6129 Remote Similarity NPD6054 Approved
0.6129 Remote Similarity NPD6059 Approved
0.6022 Remote Similarity NPD371 Approved
0.5984 Remote Similarity NPD6067 Discontinued
0.596 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5952 Remote Similarity NPD6016 Approved
0.5952 Remote Similarity NPD6015 Approved
0.5938 Remote Similarity NPD7492 Approved
0.5922 Remote Similarity NPD7525 Registered
0.5918 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5918 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5909 Remote Similarity NPD8035 Phase 2
0.5909 Remote Similarity NPD8034 Phase 2
0.5906 Remote Similarity NPD5988 Approved
0.59 Remote Similarity NPD3703 Phase 2
0.5891 Remote Similarity NPD6616 Approved
0.5887 Remote Similarity NPD7625 Phase 1
0.5882 Remote Similarity NPD6686 Approved
0.5846 Remote Similarity NPD7078 Approved
0.5827 Remote Similarity NPD8516 Approved
0.5827 Remote Similarity NPD8515 Approved
0.5827 Remote Similarity NPD8517 Approved
0.5816 Remote Similarity NPD4245 Approved
0.5816 Remote Similarity NPD4244 Approved
0.5776 Remote Similarity NPD1700 Approved
0.5763 Remote Similarity NPD4056 Clinical (unspecified phase)
0.5763 Remote Similarity NPD4057 Clinical (unspecified phase)
0.5743 Remote Similarity NPD3702 Approved
0.5739 Remote Similarity NPD7638 Approved
0.5714 Remote Similarity NPD3698 Phase 2
0.5714 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5714 Remote Similarity NPD1780 Approved
0.5714 Remote Similarity NPD1779 Approved
0.5703 Remote Similarity NPD8513 Phase 3
0.5691 Remote Similarity NPD6882 Approved
0.5691 Remote Similarity NPD8297 Approved
0.569 Remote Similarity NPD7640 Approved
0.569 Remote Similarity NPD7639 Approved
0.5682 Remote Similarity NPD6033 Approved
0.5673 Remote Similarity NPD7645 Phase 2
0.5648 Remote Similarity NPD7520 Clinical (unspecified phase)
0.5635 Remote Similarity NPD6009 Approved
0.5625 Remote Similarity NPD6319 Approved
0.561 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5604 Remote Similarity NPD2267 Suspended
0.56 Remote Similarity NPD5777 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