Structure

Physi-Chem Properties

Molecular Weight:  590.25
Volume:  568.532
LogP:  2.722
LogD:  1.326
LogS:  -2.989
# Rotatable Bonds:  10
TPSA:  154.89
# H-Bond Aceptor:  11
# H-Bond Donor:  2
# Rings:  3
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.266
Synthetic Accessibility Score:  6.446
Fsp3:  0.857
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:  -5.275
MDCK Permeability:  0.00011836663907160982
Pgp-inhibitor:  0.989
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.195
20% Bioavailability (F20%):  0.02
30% Bioavailability (F30%):  0.914

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.294
Plasma Protein Binding (PPB):  52.43738555908203%
Volume Distribution (VD):  1.451
Pgp-substrate:  24.000137329101562%

ADMET: Metabolism

CYP1A2-inhibitor:  0.011
CYP1A2-substrate:  0.027
CYP2C19-inhibitor:  0.008
CYP2C19-substrate:  0.188
CYP2C9-inhibitor:  0.004
CYP2C9-substrate:  0.015
CYP2D6-inhibitor:  0.23
CYP2D6-substrate:  0.046
CYP3A4-inhibitor:  0.321
CYP3A4-substrate:  0.353

ADMET: Excretion

Clearance (CL):  2.354
Half-life (T1/2):  0.816

ADMET: Toxicity

hERG Blockers:  0.025
Human Hepatotoxicity (H-HT):  0.958
Drug-inuced Liver Injury (DILI):  0.872
AMES Toxicity:  0.071
Rat Oral Acute Toxicity:  0.079
Maximum Recommended Daily Dose:  0.012
Skin Sensitization:  0.569
Carcinogencity:  0.118
Eye Corrosion:  0.102
Eye Irritation:  0.027
Respiratory Toxicity:  0.031

Download Data

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

  Natural Product: NPC246347

Natural Product ID:  NPC246347
Common Name*:   YMBPQCOCUHBPTR-SEQDWNMISA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  YMBPQCOCUHBPTR-SEQDWNMISA-N
Standard InCHI:  InChI=1S/C28H43ClO11/c1-13(2)20-21-22(28(35,12-29)25(38-16(5)32)23(20)37-15(4)31)18-11-26(7,34)19(36-14(3)30)9-10-27(8,24(21)39-18)40-17(6)33/h13,18-25,34-35H,9-12H2,1-8H3/t18-,19+,20-,21-,22-,23+,24-,25+,26+,27-,28-/m1/s1
SMILES:  CC(C)[C@@H]1[C@@H]2[C@@H]([C@H]3C[C@@](C)([C@H](CC[C@](C)([C@@H]2O3)OC(=O)C)OC(=O)C)O)[C@](CCl)([C@H]([C@H]1OC(=O)C)OC(=O)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2426308
PubChem CID:   73350842
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 = 6.42 % PMID[533012]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 > 10000.0 nM PMID[533012]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = 9.36 % PMID[533012]

☑ 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 NPC246347 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
0.9877 High Similarity NPC471377
0.9875 High Similarity NPC93616
0.9753 High Similarity NPC279260
0.878 High Similarity NPC186594
0.8765 High Similarity NPC43463
0.8675 High Similarity NPC211049
0.8675 High Similarity NPC119922
0.8675 High Similarity NPC116320
0.8571 High Similarity NPC216800
0.8519 High Similarity NPC136424
0.8415 Intermediate Similarity NPC476719
0.8313 Intermediate Similarity NPC191345
0.8313 Intermediate Similarity NPC252483
0.8235 Intermediate Similarity NPC470154
0.8182 Intermediate Similarity NPC228593
0.8182 Intermediate Similarity NPC235196
0.814 Intermediate Similarity NPC470155
0.814 Intermediate Similarity NPC477446
0.814 Intermediate Similarity NPC477447
0.8023 Intermediate Similarity NPC470156
0.7927 Intermediate Similarity NPC476718
0.7826 Intermediate Similarity NPC470262
0.7742 Intermediate Similarity NPC41838
0.7701 Intermediate Similarity NPC472951
0.7701 Intermediate Similarity NPC472943
0.7667 Intermediate Similarity NPC476715
0.7609 Intermediate Similarity NPC75443
0.7609 Intermediate Similarity NPC470260
0.7582 Intermediate Similarity NPC477283
0.7553 Intermediate Similarity NPC91251
0.75 Intermediate Similarity NPC110365
0.75 Intermediate Similarity NPC213658
0.75 Intermediate Similarity NPC45833
0.75 Intermediate Similarity NPC123122
0.75 Intermediate Similarity NPC44538
0.75 Intermediate Similarity NPC62202
0.7447 Intermediate Similarity NPC312471
0.7447 Intermediate Similarity NPC471378
0.7404 Intermediate Similarity NPC140409
0.7404 Intermediate Similarity NPC11491
0.7404 Intermediate Similarity NPC156248
0.7391 Intermediate Similarity NPC475684
0.7391 Intermediate Similarity NPC215968
0.7391 Intermediate Similarity NPC155531
0.7368 Intermediate Similarity NPC122057
0.7368 Intermediate Similarity NPC312805
0.7363 Intermediate Similarity NPC18953
0.734 Intermediate Similarity NPC291875
0.734 Intermediate Similarity NPC161560
0.7333 Intermediate Similarity NPC170294
0.7333 Intermediate Similarity NPC154043
0.7333 Intermediate Similarity NPC60018
0.7333 Intermediate Similarity NPC202688
0.7292 Intermediate Similarity NPC475307
0.7283 Intermediate Similarity NPC471379
0.7283 Intermediate Similarity NPC196911
0.7283 Intermediate Similarity NPC266651
0.7234 Intermediate Similarity NPC476723
0.7234 Intermediate Similarity NPC476435
0.7234 Intermediate Similarity NPC476724
0.7234 Intermediate Similarity NPC92370
0.7234 Intermediate Similarity NPC470872
0.7222 Intermediate Similarity NPC118116
0.7212 Intermediate Similarity NPC128210
0.7209 Intermediate Similarity NPC470151
0.7204 Intermediate Similarity NPC471410
0.7204 Intermediate Similarity NPC131365
0.7204 Intermediate Similarity NPC476717
0.7204 Intermediate Similarity NPC471411
0.7196 Intermediate Similarity NPC89018
0.7143 Intermediate Similarity NPC477284
0.7143 Intermediate Similarity NPC286719
0.7143 Intermediate Similarity NPC477286
0.713 Intermediate Similarity NPC226608
0.713 Intermediate Similarity NPC88867
0.7128 Intermediate Similarity NPC5943
0.7126 Intermediate Similarity NPC472950
0.7126 Intermediate Similarity NPC472952
0.7111 Intermediate Similarity NPC474714
0.71 Intermediate Similarity NPC152480
0.7097 Intermediate Similarity NPC476725
0.7083 Intermediate Similarity NPC470114
0.7065 Intermediate Similarity NPC5958
0.7065 Intermediate Similarity NPC111582
0.7065 Intermediate Similarity NPC476721
0.7065 Intermediate Similarity NPC477285
0.7065 Intermediate Similarity NPC127917
0.7065 Intermediate Similarity NPC69953
0.7065 Intermediate Similarity NPC239308
0.7065 Intermediate Similarity NPC470261
0.7064 Intermediate Similarity NPC470466
0.7053 Intermediate Similarity NPC201607
0.7053 Intermediate Similarity NPC56777
0.7053 Intermediate Similarity NPC476379
0.7033 Intermediate Similarity NPC190940
0.703 Intermediate Similarity NPC272223
0.7021 Intermediate Similarity NPC64862
0.701 Intermediate Similarity NPC473066
0.6957 Remote Similarity NPC103171
0.6939 Remote Similarity NPC122083
0.6939 Remote Similarity NPC211845
0.6939 Remote Similarity NPC256104
0.6939 Remote Similarity NPC182740
0.6923 Remote Similarity NPC471217
0.6923 Remote Similarity NPC471216
0.6923 Remote Similarity NPC186588
0.6915 Remote Similarity NPC235402
0.6915 Remote Similarity NPC477445
0.6882 Remote Similarity NPC29342
0.6882 Remote Similarity NPC2572
0.6882 Remote Similarity NPC241959
0.6875 Remote Similarity NPC471221
0.6863 Remote Similarity NPC188968
0.6857 Remote Similarity NPC470263
0.6848 Remote Similarity NPC71541
0.6848 Remote Similarity NPC77003
0.6842 Remote Similarity NPC103782
0.6842 Remote Similarity NPC114378
0.6842 Remote Similarity NPC268633
0.6842 Remote Similarity NPC474008
0.6837 Remote Similarity NPC219516
0.6832 Remote Similarity NPC111348
0.6818 Remote Similarity NPC472945
0.6818 Remote Similarity NPC472944
0.6818 Remote Similarity NPC166250
0.6813 Remote Similarity NPC477282
0.6813 Remote Similarity NPC81074
0.6813 Remote Similarity NPC477287
0.6813 Remote Similarity NPC476176
0.68 Remote Similarity NPC94582
0.68 Remote Similarity NPC57964
0.6792 Remote Similarity NPC216636
0.6792 Remote Similarity NPC319438
0.6786 Remote Similarity NPC476714
0.6774 Remote Similarity NPC208912
0.6774 Remote Similarity NPC2096
0.6742 Remote Similarity NPC186851
0.6742 Remote Similarity NPC36479
0.6739 Remote Similarity NPC16449
0.6735 Remote Similarity NPC18536
0.6735 Remote Similarity NPC475056
0.6735 Remote Similarity NPC50443
0.6733 Remote Similarity NPC237071
0.6733 Remote Similarity NPC235109
0.6733 Remote Similarity NPC203434
0.6733 Remote Similarity NPC169270
0.6733 Remote Similarity NPC292718
0.6733 Remote Similarity NPC111834
0.6733 Remote Similarity NPC306797
0.6733 Remote Similarity NPC116683
0.6733 Remote Similarity NPC238796
0.6706 Remote Similarity NPC476928
0.6703 Remote Similarity NPC272841
0.6702 Remote Similarity NPC475820
0.6702 Remote Similarity NPC474346
0.6702 Remote Similarity NPC474253
0.6702 Remote Similarity NPC474284
0.6702 Remote Similarity NPC213737
0.6701 Remote Similarity NPC309656
0.67 Remote Similarity NPC151214
0.67 Remote Similarity NPC191915
0.6699 Remote Similarity NPC51579
0.6697 Remote Similarity NPC470467
0.6696 Remote Similarity NPC282003
0.6696 Remote Similarity NPC310035
0.6696 Remote Similarity NPC188222
0.6667 Remote Similarity NPC322912
0.6667 Remote Similarity NPC293223
0.6667 Remote Similarity NPC107603
0.6667 Remote Similarity NPC274793
0.6667 Remote Similarity NPC474575
0.6667 Remote Similarity NPC216137
0.6667 Remote Similarity NPC73515
0.6667 Remote Similarity NPC475743
0.6667 Remote Similarity NPC8729
0.6667 Remote Similarity NPC214315
0.6638 Remote Similarity NPC303006
0.6636 Remote Similarity NPC470468
0.6635 Remote Similarity NPC49532
0.6635 Remote Similarity NPC98225
0.6635 Remote Similarity NPC475574
0.6635 Remote Similarity NPC472554
0.6634 Remote Similarity NPC86893
0.6634 Remote Similarity NPC292178
0.6634 Remote Similarity NPC241047
0.6634 Remote Similarity NPC476720
0.6634 Remote Similarity NPC82633
0.6633 Remote Similarity NPC477443
0.6633 Remote Similarity NPC477440
0.6632 Remote Similarity NPC477434
0.6632 Remote Similarity NPC65133
0.6632 Remote Similarity NPC473299
0.6632 Remote Similarity NPC320824
0.6602 Remote Similarity NPC209798
0.6602 Remote Similarity NPC471375
0.6602 Remote Similarity NPC472144
0.6602 Remote Similarity NPC292775
0.6602 Remote Similarity NPC471374
0.6598 Remote Similarity NPC472396
0.6593 Remote Similarity NPC474574

  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 NPC246347 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
0.7059 Intermediate Similarity NPD7532 Clinical (unspecified phase)
0.6747 Remote Similarity NPD371 Approved
0.6354 Remote Similarity NPD3670 Clinical (unspecified phase)
0.6354 Remote Similarity NPD3669 Approved
0.6168 Remote Similarity NPD1700 Approved
0.6111 Remote Similarity NPD3653 Clinical (unspecified phase)
0.6019 Remote Similarity NPD5344 Discontinued
0.6 Remote Similarity NPD6115 Approved
0.6 Remote Similarity NPD6118 Approved
0.6 Remote Similarity NPD6697 Approved
0.6 Remote Similarity NPD4267 Clinical (unspecified phase)
0.6 Remote Similarity NPD6114 Approved
0.5982 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5962 Remote Similarity NPD8171 Discontinued
0.5929 Remote Similarity NPD4061 Clinical (unspecified phase)
0.5914 Remote Similarity NPD1810 Approved
0.5914 Remote Similarity NPD1811 Approved
0.5895 Remote Similarity NPD6116 Phase 1
0.5877 Remote Similarity NPD5955 Clinical (unspecified phase)
0.5789 Remote Similarity NPD6117 Approved
0.5789 Remote Similarity NPD8132 Clinical (unspecified phase)
0.578 Remote Similarity NPD6648 Approved
0.5761 Remote Similarity NPD2254 Approved
0.5761 Remote Similarity NPD2686 Approved
0.5761 Remote Similarity NPD2687 Approved
0.575 Remote Similarity NPD7516 Approved
0.5714 Remote Similarity NPD6928 Phase 2
0.5714 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5682 Remote Similarity NPD847 Phase 1
0.5667 Remote Similarity NPD7328 Approved
0.5667 Remote Similarity NPD7327 Approved
0.5657 Remote Similarity NPD1780 Approved
0.5657 Remote Similarity NPD1779 Approved
0.5656 Remote Similarity NPD5983 Phase 2
0.5614 Remote Similarity NPD5954 Clinical (unspecified phase)
0.56 Remote Similarity NPD6336 Discontinued

  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