Structure

Physi-Chem Properties

Molecular Weight:  780.32
Volume:  713.667
LogP:  -2.988
LogD:  -2.597
LogS:  -0.735
# Rotatable Bonds:  19
TPSA:  324.06
# H-Bond Aceptor:  21
# H-Bond Donor:  11
# Rings:  4
# Heavy Atoms:  22

MedChem Properties

QED Drug-Likeness Score:  0.032
Synthetic Accessibility Score:  5.53
Fsp3:  0.806
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.514
MDCK Permeability:  0.00016869493992999196
Pgp-inhibitor:  0.0
Pgp-substrate:  0.777
Human Intestinal Absorption (HIA):  0.999
20% Bioavailability (F20%):  0.999
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.16
Plasma Protein Binding (PPB):  26.469873428344727%
Volume Distribution (VD):  0.359
Pgp-substrate:  58.737247467041016%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.011
CYP2C19-inhibitor:  0.014
CYP2C19-substrate:  0.037
CYP2C9-inhibitor:  0.005
CYP2C9-substrate:  0.027
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.067
CYP3A4-inhibitor:  0.005
CYP3A4-substrate:  0.004

ADMET: Excretion

Clearance (CL):  0.982
Half-life (T1/2):  0.653

ADMET: Toxicity

hERG Blockers:  0.076
Human Hepatotoxicity (H-HT):  0.291
Drug-inuced Liver Injury (DILI):  0.528
AMES Toxicity:  0.05
Rat Oral Acute Toxicity:  0.027
Maximum Recommended Daily Dose:  0.371
Skin Sensitization:  0.195
Carcinogencity:  0.924
Eye Corrosion:  0.003
Eye Irritation:  0.004
Respiratory Toxicity:  0.924

Download Data

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

  Natural Product: NPC477398

Natural Product ID:  NPC477398
Common Name*:   dysinosin B
IUPAC Name:   [(2R)-3-[[(2S)-1-[(2S,3aR,5S,6S,7aS)-2-[2-[1-(diaminomethylidene)-2,5-dihydropyrrol-1-ium-3-yl]ethylcarbamoyl]-5-hydroxy-6-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-2,3,3a,4,5,6,7,7a-octahydroindol-1-yl]-3-methyl-1-oxobutan-2-yl]amino]-2-methoxy-3-oxopropyl] sulfate
Synonyms:  
Standard InCHIKey:  RPYXLWOZBBICPU-CVAXQKIFSA-N
Standard InCHI:  InChI=1S/C31H52N6O15S/c1-14(2)23(35-28(44)22(49-3)13-50-53(46,47)48)29(45)37-17-10-20(51-30-26(42)25(41)24(40)21(12-38)52-30)19(39)9-16(17)8-18(37)27(43)34-6-4-15-5-7-36(11-15)31(32)33/h5,14,16-26,30,38-42H,4,6-13H2,1-3H3,(H6,32,33,34,35,43,44,46,47,48)/t16-,17+,18+,19+,20+,21-,22-,23+,24-,25+,26-,30+/m1/s1
SMILES:  CC(C)[C@@H](C(=O)N1[C@H]2C[C@@H]([C@H](C[C@H]2C[C@H]1C(=O)NCCC3=CC[N+](=C(N)N)C3)O)O[C@@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)NC(=O)[C@@H](COS(=O)(=O)[O-])OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   11274304
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000348] Peptides
            • [CHEMONTID:0004830] Dipeptides

*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
NPO17682 Lamellodysidea chlorea Species Dysideidae Eukaryota n.a. n.a. n.a. PMID[15332844]
NPO17682 Lamellodysidea chlorea Species Dysideidae 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
NPT6254 Individual Protein Coagulation factor VII Homo sapiens Ki = 90 nM PMID[15332844]
NPT670 Individual Protein Thrombin Homo sapiens Ki = 170 nM PMID[15332844]

☑ 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 NPC477398 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
0.9085 High Similarity NPC477399
0.9085 High Similarity NPC477401
0.8732 High Similarity NPC477400
0.6776 Remote Similarity NPC471255
0.6601 Remote Similarity NPC471262
0.6474 Remote Similarity NPC471263
0.646 Remote Similarity NPC471256
0.6379 Remote Similarity NPC316244
0.6348 Remote Similarity NPC5719
0.6348 Remote Similarity NPC22883
0.6348 Remote Similarity NPC210377
0.6348 Remote Similarity NPC217804
0.6278 Remote Similarity NPC63040
0.6222 Remote Similarity NPC15068
0.619 Remote Similarity NPC304299
0.619 Remote Similarity NPC475278
0.619 Remote Similarity NPC247776
0.619 Remote Similarity NPC309450
0.619 Remote Similarity NPC475266
0.6149 Remote Similarity NPC475918
0.6124 Remote Similarity NPC1390
0.6124 Remote Similarity NPC62104
0.6095 Remote Similarity NPC71866
0.6076 Remote Similarity NPC20035
0.6074 Remote Similarity NPC475472
0.6071 Remote Similarity NPC315210
0.6071 Remote Similarity NPC315848
0.6067 Remote Similarity NPC197743
0.6067 Remote Similarity NPC319334
0.6067 Remote Similarity NPC322372
0.6067 Remote Similarity NPC297145
0.6067 Remote Similarity NPC327517
0.6062 Remote Similarity NPC309525
0.6059 Remote Similarity NPC142761
0.6037 Remote Similarity NPC119794
0.6037 Remote Similarity NPC73829
0.6034 Remote Similarity NPC2501
0.6023 Remote Similarity NPC122590
0.6022 Remote Similarity NPC477462
0.6012 Remote Similarity NPC180770
0.6 Remote Similarity NPC76999
0.6 Remote Similarity NPC120420
0.6 Remote Similarity NPC470654
0.6 Remote Similarity NPC470650
0.6 Remote Similarity NPC470653
0.6 Remote Similarity NPC471527
0.5978 Remote Similarity NPC321485
0.5978 Remote Similarity NPC317377
0.5976 Remote Similarity NPC82931
0.5976 Remote Similarity NPC120335
0.5976 Remote Similarity NPC172365
0.5976 Remote Similarity NPC210729
0.5975 Remote Similarity NPC273185
0.5965 Remote Similarity NPC141669
0.5964 Remote Similarity NPC75318
0.5964 Remote Similarity NPC280941
0.5964 Remote Similarity NPC235772
0.5964 Remote Similarity NPC99864
0.5951 Remote Similarity NPC313962
0.5948 Remote Similarity NPC476875
0.5941 Remote Similarity NPC162910
0.593 Remote Similarity NPC52748
0.5928 Remote Similarity NPC145899
0.5917 Remote Similarity NPC302276
0.5912 Remote Similarity NPC160688
0.5906 Remote Similarity NPC476877
0.5906 Remote Similarity NPC475584
0.5906 Remote Similarity NPC475394
0.5906 Remote Similarity NPC475152
0.5888 Remote Similarity NPC302715
0.5886 Remote Similarity NPC471821
0.5886 Remote Similarity NPC471820
0.5879 Remote Similarity NPC139585
0.5879 Remote Similarity NPC73655
0.5876 Remote Similarity NPC94862
0.5872 Remote Similarity NPC69176
0.5872 Remote Similarity NPC193579
0.5872 Remote Similarity NPC284625
0.5872 Remote Similarity NPC475892
0.5872 Remote Similarity NPC298469
0.586 Remote Similarity NPC477121
0.5858 Remote Similarity NPC243680
0.5858 Remote Similarity NPC200788
0.5849 Remote Similarity NPC470652
0.5847 Remote Similarity NPC471052
0.5847 Remote Similarity NPC471053
0.5847 Remote Similarity NPC471051
0.5846 Remote Similarity NPC102959
0.5838 Remote Similarity NPC298067
0.5838 Remote Similarity NPC214821
0.5828 Remote Similarity NPC476876
0.5816 Remote Similarity NPC60516
0.5813 Remote Similarity NPC315188
0.5808 Remote Similarity NPC477072
0.5805 Remote Similarity NPC315266
0.5796 Remote Similarity NPC296043
0.5786 Remote Similarity NPC477237
0.5779 Remote Similarity NPC121479
0.5779 Remote Similarity NPC57436
0.5776 Remote Similarity NPC94319
0.5771 Remote Similarity NPC477552
0.5771 Remote Similarity NPC61717
0.5771 Remote Similarity NPC244380
0.5771 Remote Similarity NPC477550
0.5767 Remote Similarity NPC315058
0.5759 Remote Similarity NPC329216
0.5747 Remote Similarity NPC276822
0.574 Remote Similarity NPC82129
0.5732 Remote Similarity NPC103391
0.5732 Remote Similarity NPC472536
0.5731 Remote Similarity NPC265908
0.5724 Remote Similarity NPC241394
0.5714 Remote Similarity NPC242728
0.5714 Remote Similarity NPC318142
0.5714 Remote Similarity NPC477238
0.5714 Remote Similarity NPC477551
0.5706 Remote Similarity NPC36254
0.5706 Remote Similarity NPC36463
0.5706 Remote Similarity NPC298005
0.5705 Remote Similarity NPC478024
0.5698 Remote Similarity NPC314050
0.5698 Remote Similarity NPC315809
0.5682 Remote Similarity NPC262077
0.5677 Remote Similarity NPC251122
0.5677 Remote Similarity NPC97526
0.5677 Remote Similarity NPC119652
0.5663 Remote Similarity NPC25327
0.5658 Remote Similarity NPC128303
0.5655 Remote Similarity NPC314361
0.5649 Remote Similarity NPC171734
0.5649 Remote Similarity NPC207820
0.5647 Remote Similarity NPC472430
0.5638 Remote Similarity NPC280022
0.5633 Remote Similarity NPC259586
0.5629 Remote Similarity NPC477198
0.5625 Remote Similarity NPC477519
0.5622 Remote Similarity NPC80514
0.5614 Remote Similarity NPC473683
0.5611 Remote Similarity NPC162104
0.5611 Remote Similarity NPC265699
0.5611 Remote Similarity NPC300443
0.5611 Remote Similarity NPC475527
0.5602 Remote Similarity NPC470651
0.5602 Remote Similarity NPC470655
0.5602 Remote Similarity NPC471165

  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 NPC477398 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
0.6144 Remote Similarity NPD3204 Clinical (unspecified phase)
0.6076 Remote Similarity NPD6436 Phase 3
0.6024 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5964 Remote Similarity NPD8415 Approved
0.5864 Remote Similarity NPD4816 Clinical (unspecified phase)
0.586 Remote Similarity NPD6935 Phase 3
0.586 Remote Similarity NPD6936 Clinical (unspecified phase)
0.5848 Remote Similarity NPD6077 Discontinued
0.5779 Remote Similarity NPD4833 Approved
0.5779 Remote Similarity NPD35 Approved
0.5778 Remote Similarity NPD8414 Discontinued
0.5776 Remote Similarity NPD4827 Approved
0.5776 Remote Similarity NPD4828 Approved
0.5776 Remote Similarity NPD4826 Approved
0.5762 Remote Similarity NPD2700 Approved
0.5759 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5723 Remote Similarity NPD6918 Phase 1
0.5696 Remote Similarity NPD4831 Approved
0.5696 Remote Similarity NPD4832 Approved
0.5696 Remote Similarity NPD4830 Approved
0.5695 Remote Similarity NPD6122 Discontinued
0.5687 Remote Similarity NPD2132 Phase 3
0.5617 Remote Similarity NPD8274 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