Structure

Physi-Chem Properties

Molecular Weight:  532.24
Volume:  518.996
LogP:  3.319
LogD:  1.581
LogS:  -3.271
# Rotatable Bonds:  8
TPSA:  128.59
# H-Bond Aceptor:  9
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.312
Synthetic Accessibility Score:  6.346
Fsp3:  0.885
Lipinski Rule-of-5:  Accepted
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:  -5.146
MDCK Permeability:  9.534399578114972e-05
Pgp-inhibitor:  0.984
Pgp-substrate:  0.003
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.011
30% Bioavailability (F30%):  0.409

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.277
Plasma Protein Binding (PPB):  71.36944580078125%
Volume Distribution (VD):  1.401
Pgp-substrate:  21.685361862182617%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.037
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.416
CYP2C9-inhibitor:  0.01
CYP2C9-substrate:  0.02
CYP2D6-inhibitor:  0.02
CYP2D6-substrate:  0.048
CYP3A4-inhibitor:  0.322
CYP3A4-substrate:  0.364

ADMET: Excretion

Clearance (CL):  2.866
Half-life (T1/2):  0.784

ADMET: Toxicity

hERG Blockers:  0.084
Human Hepatotoxicity (H-HT):  0.883
Drug-inuced Liver Injury (DILI):  0.884
AMES Toxicity:  0.112
Rat Oral Acute Toxicity:  0.044
Maximum Recommended Daily Dose:  0.014
Skin Sensitization:  0.542
Carcinogencity:  0.171
Eye Corrosion:  0.207
Eye Irritation:  0.062
Respiratory Toxicity:  0.123

Download Data

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

  Natural Product: NPC93616

Natural Product ID:  NPC93616
Common Name*:   MYALRPVEAYVMAK-VIGGNCANSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  MYALRPVEAYVMAK-VIGGNCANSA-N
Standard InCHI:  InChI=1S/C26H41ClO9/c1-13(2)17-10-20(34-15(4)29)26(32,12-27)22-18-11-24(6,31)19(33-14(3)28)8-9-25(7,36-16(5)30)23(35-18)21(17)22/h13,17-23,31-32H,8-12H2,1-7H3/t17-,18-,19+,20+,21-,22-,23-,24+,25-,26+/m1/s1
SMILES:  CC(C)[C@H]1C[C@@H]([C@@](CCl)([C@@H]2[C@H]3C[C@@](C)([C@H](CC[C@](C)([C@@H]([C@H]12)O3)OC(=O)C)OC(=O)C)O)O)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2426310
PubChem CID:   73353795
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0002916] Eunicellane and asbestinane 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
NPO16055 Klyxum molle Species Alcyoniidae Eukaryota n.a. n.a. n.a. PMID[22004052]
NPO16055 Klyxum molle Species Alcyoniidae Eukaryota n.a. Formosan soft coral n.a. PMID[24020806]
NPO16055 Klyxum molle Species Alcyoniidae 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
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = -1.19 % PMID[558313]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 10000.0 nM PMID[558313]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = 8.92 % PMID[558313]

☑ 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 NPC93616 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
0.9875 High Similarity NPC279260
0.9875 High Similarity NPC246347
0.9753 High Similarity NPC471377
0.8659 High Similarity NPC186594
0.8642 High Similarity NPC43463
0.8625 High Similarity NPC136424
0.8554 High Similarity NPC119922
0.8554 High Similarity NPC116320
0.8554 High Similarity NPC211049
0.8519 High Similarity NPC476719
0.8452 Intermediate Similarity NPC216800
0.8415 Intermediate Similarity NPC191345
0.8415 Intermediate Similarity NPC252483
0.8118 Intermediate Similarity NPC470154
0.8068 Intermediate Similarity NPC235196
0.8068 Intermediate Similarity NPC228593
0.8025 Intermediate Similarity NPC476718
0.8023 Intermediate Similarity NPC470155
0.8023 Intermediate Similarity NPC477446
0.8023 Intermediate Similarity NPC477447
0.7907 Intermediate Similarity NPC470156
0.7791 Intermediate Similarity NPC472951
0.7791 Intermediate Similarity NPC472943
0.7753 Intermediate Similarity NPC476715
0.7717 Intermediate Similarity NPC470262
0.7692 Intermediate Similarity NPC470260
0.7692 Intermediate Similarity NPC75443
0.7634 Intermediate Similarity NPC41838
0.759 Intermediate Similarity NPC123122
0.7527 Intermediate Similarity NPC471378
0.7527 Intermediate Similarity NPC312471
0.7473 Intermediate Similarity NPC475684
0.7473 Intermediate Similarity NPC477283
0.7447 Intermediate Similarity NPC122057
0.7447 Intermediate Similarity NPC312805
0.7447 Intermediate Similarity NPC91251
0.7444 Intermediate Similarity NPC18953
0.7419 Intermediate Similarity NPC161560
0.7391 Intermediate Similarity NPC110365
0.7391 Intermediate Similarity NPC44538
0.7391 Intermediate Similarity NPC62202
0.7391 Intermediate Similarity NPC213658
0.7391 Intermediate Similarity NPC45833
0.7363 Intermediate Similarity NPC471379
0.7363 Intermediate Similarity NPC196911
0.7312 Intermediate Similarity NPC92370
0.7312 Intermediate Similarity NPC476723
0.7312 Intermediate Similarity NPC476724
0.7312 Intermediate Similarity NPC470872
0.7308 Intermediate Similarity NPC140409
0.7308 Intermediate Similarity NPC156248
0.7308 Intermediate Similarity NPC11491
0.7303 Intermediate Similarity NPC118116
0.7283 Intermediate Similarity NPC215968
0.7283 Intermediate Similarity NPC476717
0.7283 Intermediate Similarity NPC471411
0.7283 Intermediate Similarity NPC471410
0.7283 Intermediate Similarity NPC155531
0.7282 Intermediate Similarity NPC128210
0.7238 Intermediate Similarity NPC170294
0.7234 Intermediate Similarity NPC291875
0.7222 Intermediate Similarity NPC154043
0.7222 Intermediate Similarity NPC60018
0.7222 Intermediate Similarity NPC202688
0.7222 Intermediate Similarity NPC286719
0.7222 Intermediate Similarity NPC477286
0.7209 Intermediate Similarity NPC472950
0.7209 Intermediate Similarity NPC472952
0.7188 Intermediate Similarity NPC475307
0.7174 Intermediate Similarity NPC476725
0.7174 Intermediate Similarity NPC266651
0.7143 Intermediate Similarity NPC470261
0.7143 Intermediate Similarity NPC5958
0.7143 Intermediate Similarity NPC476721
0.7143 Intermediate Similarity NPC111582
0.7143 Intermediate Similarity NPC477285
0.7143 Intermediate Similarity NPC127917
0.7143 Intermediate Similarity NPC239308
0.7128 Intermediate Similarity NPC201607
0.7128 Intermediate Similarity NPC56777
0.7128 Intermediate Similarity NPC476435
0.7111 Intermediate Similarity NPC190940
0.7103 Intermediate Similarity NPC89018
0.7097 Intermediate Similarity NPC64862
0.7097 Intermediate Similarity NPC131365
0.7093 Intermediate Similarity NPC470151
0.7083 Intermediate Similarity NPC473066
0.7037 Intermediate Similarity NPC226608
0.7037 Intermediate Similarity NPC88867
0.7033 Intermediate Similarity NPC477284
0.7033 Intermediate Similarity NPC103171
0.7021 Intermediate Similarity NPC5943
0.701 Intermediate Similarity NPC122083
0.701 Intermediate Similarity NPC211845
0.701 Intermediate Similarity NPC182740
0.701 Intermediate Similarity NPC256104
0.7 Intermediate Similarity NPC152480
0.7 Intermediate Similarity NPC471216
0.7 Intermediate Similarity NPC471217
0.7 Intermediate Similarity NPC474714
0.6989 Remote Similarity NPC235402
0.6979 Remote Similarity NPC470114
0.6972 Remote Similarity NPC470466
0.6957 Remote Similarity NPC69953
0.6957 Remote Similarity NPC29342
0.6957 Remote Similarity NPC2572
0.6947 Remote Similarity NPC471221
0.6947 Remote Similarity NPC476379
0.6931 Remote Similarity NPC272223
0.6923 Remote Similarity NPC71541
0.6923 Remote Similarity NPC77003
0.6915 Remote Similarity NPC103782
0.6915 Remote Similarity NPC114378
0.6915 Remote Similarity NPC474008
0.6897 Remote Similarity NPC166250
0.6897 Remote Similarity NPC472944
0.6897 Remote Similarity NPC472945
0.6889 Remote Similarity NPC477287
0.6889 Remote Similarity NPC476176
0.6869 Remote Similarity NPC57964
0.6869 Remote Similarity NPC94582
0.6857 Remote Similarity NPC319438
0.6857 Remote Similarity NPC216636
0.6848 Remote Similarity NPC2096
0.6848 Remote Similarity NPC208912
0.6818 Remote Similarity NPC36479
0.6818 Remote Similarity NPC186851
0.6813 Remote Similarity NPC186588
0.6809 Remote Similarity NPC477445
0.6804 Remote Similarity NPC50443
0.6804 Remote Similarity NPC18536
0.6804 Remote Similarity NPC475056
0.68 Remote Similarity NPC203434
0.68 Remote Similarity NPC237071
0.68 Remote Similarity NPC238796
0.6786 Remote Similarity NPC476928
0.6778 Remote Similarity NPC272841
0.6774 Remote Similarity NPC213737
0.6774 Remote Similarity NPC474284
0.6774 Remote Similarity NPC475820
0.6774 Remote Similarity NPC474253
0.6774 Remote Similarity NPC474346
0.6774 Remote Similarity NPC241959
0.6771 Remote Similarity NPC309656
0.6768 Remote Similarity NPC191915
0.6768 Remote Similarity NPC151214
0.6765 Remote Similarity NPC51579
0.6765 Remote Similarity NPC188968
0.6762 Remote Similarity NPC470263
0.6742 Remote Similarity NPC293223
0.6739 Remote Similarity NPC73515
0.6737 Remote Similarity NPC268633
0.6737 Remote Similarity NPC214315
0.6735 Remote Similarity NPC219516
0.6735 Remote Similarity NPC8729
0.6733 Remote Similarity NPC111348
0.6729 Remote Similarity NPC322912
0.6703 Remote Similarity NPC477282
0.6703 Remote Similarity NPC81074
0.6702 Remote Similarity NPC473299
0.6702 Remote Similarity NPC477434
0.6702 Remote Similarity NPC65133
0.6701 Remote Similarity NPC477443
0.6701 Remote Similarity NPC477440
0.67 Remote Similarity NPC476720
0.6696 Remote Similarity NPC476714
0.6667 Remote Similarity NPC64081
0.6667 Remote Similarity NPC471375
0.6667 Remote Similarity NPC11907
0.6667 Remote Similarity NPC474574
0.6667 Remote Similarity NPC209798
0.6667 Remote Similarity NPC292775
0.6667 Remote Similarity NPC133596
0.6667 Remote Similarity NPC212453
0.6667 Remote Similarity NPC471374
0.6634 Remote Similarity NPC111834
0.6634 Remote Similarity NPC252056
0.6634 Remote Similarity NPC169270
0.6634 Remote Similarity NPC306797
0.6634 Remote Similarity NPC292718
0.6634 Remote Similarity NPC475785
0.6634 Remote Similarity NPC156377
0.6634 Remote Similarity NPC116683
0.6634 Remote Similarity NPC475765
0.6634 Remote Similarity NPC235109
0.6633 Remote Similarity NPC477444
0.6633 Remote Similarity NPC185529
0.6633 Remote Similarity NPC477442
0.6633 Remote Similarity NPC477433
0.6633 Remote Similarity NPC472146
0.6632 Remote Similarity NPC478111
0.6632 Remote Similarity NPC469555
0.663 Remote Similarity NPC16449
0.6628 Remote Similarity NPC470833
0.6609 Remote Similarity NPC310035
0.6609 Remote Similarity NPC188222
0.6609 Remote Similarity NPC282003
0.6606 Remote Similarity NPC470467
0.6602 Remote Similarity NPC471426
0.6602 Remote Similarity NPC471428

  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 NPC93616 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
0.6941 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6627 Remote Similarity NPD371 Approved
0.6421 Remote Similarity NPD3670 Clinical (unspecified phase)
0.6421 Remote Similarity NPD3669 Approved
0.6075 Remote Similarity NPD1700 Approved
0.6067 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6064 Remote Similarity NPD6114 Approved
0.6064 Remote Similarity NPD6697 Approved
0.6064 Remote Similarity NPD6118 Approved
0.6064 Remote Similarity NPD6115 Approved
0.6019 Remote Similarity NPD3653 Clinical (unspecified phase)
0.6019 Remote Similarity NPD8171 Discontinued
0.5978 Remote Similarity NPD1811 Approved
0.5978 Remote Similarity NPD1810 Approved
0.5957 Remote Similarity NPD6116 Phase 1
0.5926 Remote Similarity NPD5344 Discontinued
0.5893 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5851 Remote Similarity NPD6117 Approved
0.5841 Remote Similarity NPD4061 Clinical (unspecified phase)
0.5841 Remote Similarity NPD8132 Clinical (unspecified phase)
0.5824 Remote Similarity NPD2254 Approved
0.5824 Remote Similarity NPD2686 Approved
0.5824 Remote Similarity NPD2687 Approved
0.5789 Remote Similarity NPD5955 Clinical (unspecified phase)
0.5773 Remote Similarity NPD6928 Phase 2
0.5766 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5747 Remote Similarity NPD847 Phase 1
0.5714 Remote Similarity NPD1780 Approved
0.5714 Remote Similarity NPD1779 Approved
0.5702 Remote Similarity NPD5983 Phase 2
0.5688 Remote Similarity NPD6648 Approved
0.5667 Remote Similarity NPD7516 Approved
0.5645 Remote Similarity NPD6336 Discontinued
0.5641 Remote Similarity NPD8133 Approved
0.5641 Remote Similarity NPD4632 Approved
0.5638 Remote Similarity NPD6113 Clinical (unspecified phase)

  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