NPASS Compound

Structure

CID79367 OpenBabel06191715412D 34 34 0 0 1 0 0 0 0 0999 V2000 -9.5498 -17.7808 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.5008 -17.4718 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.7087 -16.4936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.9656 -15.8245 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.1735 -14.8464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.4303 -14.1772 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.6383 -13.1991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8951 -12.5299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.1030 -11.5518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3599 -10.8827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5678 -9.9045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8246 -9.2354 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.0326 -8.2572 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2894 -7.5881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1485 -0.9990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1974 -1.3080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4973 -6.6100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8916 -1.6681 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4543 -0.6389 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7542 -5.9408 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6837 -2.6463 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5032 -0.9479 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9621 -4.9627 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4269 -3.3154 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7601 -0.2788 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8090 -0.5878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2189 -4.2936 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5000 -1.5388 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8090 -0.5878 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.5000 -1.5388 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2679 -4.6026 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1.0878 -2.3479 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -1.0878 -2.3479 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 13 14 1 0 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 15 18 2 0 0 0 0 16 19 1 0 0 0 0 17 20 1 0 0 0 0 18 21 1 0 0 0 0 19 22 1 0 0 0 0 20 23 1 0 0 0 0 21 24 1 0 0 0 0 22 25 1 0 0 0 0 23 27 2 0 0 0 0 24 27 1 0 0 0 0 26 28 1 0 0 0 0 26 34 1 0 0 0 0 27 31 1 0 0 0 0 28 30 1 0 0 0 0 28 32 1 6 0 0 0 29 25 1 6 0 0 0 29 30 1 0 0 0 0 29 34 1 0 0 0 0 30 33 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	497.4
Volume:	557.395
LogP:	8.87
LogD:	5.056
LogS:	-3.197
# Rotatable Bonds:	23
TPSA:	55.48
# H-Bond Aceptor:	3
# H-Bond Donor:	3
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.109
Synthetic Accessibility Score:	3.961
Fsp3:	0.867
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-5.156
MDCK Permeability:	2.6183797672274522e-05
Pgp-inhibitor:	0.0
Pgp-substrate:	0.006
Human Intestinal Absorption (HIA):	0.444
20% Bioavailability (F20%):	1.0
30% Bioavailability (F30%):	0.983

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003
Plasma Protein Binding (PPB):	99.8053207397461%
Volume Distribution (VD):	2.033
Pgp-substrate:	0.42930692434310913%

ADMET: Metabolism

CYP1A2-inhibitor:	0.061
CYP1A2-substrate:	0.192
CYP2C19-inhibitor:	0.191
CYP2C19-substrate:	0.057
CYP2C9-inhibitor:	0.052
CYP2C9-substrate:	0.771
CYP2D6-inhibitor:	0.754
CYP2D6-substrate:	0.901
CYP3A4-inhibitor:	0.345
CYP3A4-substrate:	0.06

ADMET: Excretion

Clearance (CL):	4.107
Half-life (T1/2):	0.206

ADMET: Toxicity

hERG Blockers:	0.957
Human Hepatotoxicity (H-HT):	0.467
Drug-inuced Liver Injury (DILI):	0.096
AMES Toxicity:	0.296
Rat Oral Acute Toxicity:	0.075
Maximum Recommended Daily Dose:	0.215
Skin Sensitization:	0.98
Carcinogencity:	0.206
Eye Corrosion:	0.6
Eye Irritation:	0.163
Respiratory Toxicity:	0.959

Download Data

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

Natural Product: NPC79367

Natural Product ID:	NPC79367
*Common Name:**	Penasin B
IUPAC Name:	(2S,3S,4S)-4-amino-2-[(5Z,9Z)-9-chlorohexacosa-5,9-dienyl]oxolan-3-ol
Synonyms:	Penasin B
Standard InCHIKey:	MOBARKDTJFXOAP-BDGGXDINSA-N
Standard InCHI:	InChI=1S/C30H56ClNO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-17-20-23-27(31)24-21-18-15-16-19-22-25-29-30(33)28(32)26-34-29/h15,18,23,28-30,33H,2-14,16-17,19-22,24-26,32H2,1H3/b18-15-,27-23-/t28-,29-,30-/m0/s1
SMILES:	CCCCCCCCCCCCCCCC/C=C(/CC/C=CCCCC[C@H]1[C@H]([C@H](CO1)N)O)Cl
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1641874
PubChem CID:	50901044
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0002648] Tetrahydrofurans

*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
NPO31241	Penares	Genus	Geodiidae	Eukaryota	n.a.	n.a.	n.a.	PMID[20949915]

☑ 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

Activity Type	# Activity
IC50	2

Activity Type	# Activity
Cell Line	2

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	10.0	ug.mL-1	PMID[502925]
NPT168	Cell Line	P388	Mus musculus	IC50	=	50.0	ug.mL-1	PMID[502925]

☑ 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 NPC79367 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	57
0.1-0.2	1023
0.2-0.3	20887
0.3-0.4	15557
0.4-0.5	4644
0.5-0.6	485
0.6-0.7	34
0.7-0.8	8
0.8-0.85	0
0.85-0.9	0
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9324	High Similarity	NPC3094
0.7763	Intermediate Similarity	NPC113224
0.7703	Intermediate Similarity	NPC17455
0.7703	Intermediate Similarity	NPC47333
0.7654	Intermediate Similarity	NPC51055
0.7654	Intermediate Similarity	NPC140327
0.7654	Intermediate Similarity	NPC62293
0.7654	Intermediate Similarity	NPC212008
0.7209	Intermediate Similarity	NPC207657
0.7162	Intermediate Similarity	NPC168308
0.7162	Intermediate Similarity	NPC302569
0.7143	Intermediate Similarity	NPC55068
0.7024	Intermediate Similarity	NPC264417
0.7024	Intermediate Similarity	NPC217095
0.6977	Remote Similarity	NPC474833
0.68	Remote Similarity	NPC8979
0.6782	Remote Similarity	NPC473972
0.6782	Remote Similarity	NPC473971
0.6782	Remote Similarity	NPC475363
0.6588	Remote Similarity	NPC305223
0.6562	Remote Similarity	NPC475603
0.6562	Remote Similarity	NPC61894
0.6548	Remote Similarity	NPC324638
0.6512	Remote Similarity	NPC477422
0.6512	Remote Similarity	NPC288086
0.6486	Remote Similarity	NPC123814
0.6429	Remote Similarity	NPC291196
0.6429	Remote Similarity	NPC103712
0.6354	Remote Similarity	NPC39290
0.6354	Remote Similarity	NPC159369
0.6344	Remote Similarity	NPC477199
0.631	Remote Similarity	NPC474812
0.6267	Remote Similarity	NPC474322
0.6235	Remote Similarity	NPC475930
0.6235	Remote Similarity	NPC127145
0.6207	Remote Similarity	NPC26932
0.6163	Remote Similarity	NPC474674
0.6154	Remote Similarity	NPC314762
0.6136	Remote Similarity	NPC473588
0.6136	Remote Similarity	NPC78562
0.6129	Remote Similarity	NPC474312
0.6125	Remote Similarity	NPC325550
0.6125	Remote Similarity	NPC329003
0.6125	Remote Similarity	NPC326524
0.6122	Remote Similarity	NPC139782
0.6122	Remote Similarity	NPC74672
0.6122	Remote Similarity	NPC43074
0.6122	Remote Similarity	NPC209047
0.6122	Remote Similarity	NPC242503
0.6061	Remote Similarity	NPC263545
0.6061	Remote Similarity	NPC15851
0.6061	Remote Similarity	NPC186840
0.6061	Remote Similarity	NPC475125
0.6061	Remote Similarity	NPC473581
0.6061	Remote Similarity	NPC473950
0.6061	Remote Similarity	NPC309898
0.6061	Remote Similarity	NPC473604
0.6061	Remote Similarity	NPC111567
0.6047	Remote Similarity	NPC474675
0.6047	Remote Similarity	NPC137620
0.6042	Remote Similarity	NPC258824
0.6019	Remote Similarity	NPC315170
0.6	Remote Similarity	NPC477198
0.6	Remote Similarity	NPC22101
0.6	Remote Similarity	NPC127091
0.6	Remote Similarity	NPC330426
0.6	Remote Similarity	NPC321030
0.6	Remote Similarity	NPC271921
0.6	Remote Similarity	NPC104537
0.6	Remote Similarity	NPC148192
0.5946	Remote Similarity	NPC96966
0.5946	Remote Similarity	NPC121062
0.5946	Remote Similarity	NPC29222
0.5941	Remote Similarity	NPC156782
0.5941	Remote Similarity	NPC256570
0.5941	Remote Similarity	NPC3568
0.5941	Remote Similarity	NPC54961
0.5941	Remote Similarity	NPC282088
0.5941	Remote Similarity	NPC157353
0.5941	Remote Similarity	NPC192066
0.5941	Remote Similarity	NPC158445
0.5941	Remote Similarity	NPC17290
0.593	Remote Similarity	NPC48218
0.593	Remote Similarity	NPC141481
0.593	Remote Similarity	NPC473559
0.593	Remote Similarity	NPC324981
0.5926	Remote Similarity	NPC319131
0.5909	Remote Similarity	NPC474468
0.59	Remote Similarity	NPC182632
0.59	Remote Similarity	NPC282705
0.5895	Remote Similarity	NPC178758
0.5895	Remote Similarity	NPC196102
0.5895	Remote Similarity	NPC228638
0.5882	Remote Similarity	NPC476261
0.5882	Remote Similarity	NPC25033
0.5882	Remote Similarity	NPC470382
0.5882	Remote Similarity	NPC471635
0.5882	Remote Similarity	NPC119225
0.5882	Remote Similarity	NPC83965
0.5862	Remote Similarity	NPC475694
0.5862	Remote Similarity	NPC473710
0.5862	Remote Similarity	NPC16964
0.5843	Remote Similarity	NPC476709
0.5833	Remote Similarity	NPC475918
0.5825	Remote Similarity	NPC8098
0.5825	Remote Similarity	NPC183449
0.5825	Remote Similarity	NPC197294
0.5814	Remote Similarity	NPC475443
0.5814	Remote Similarity	NPC473829
0.5804	Remote Similarity	NPC314306
0.5795	Remote Similarity	NPC476696
0.5795	Remote Similarity	NPC476695
0.5795	Remote Similarity	NPC476694
0.5795	Remote Similarity	NPC476660
0.5795	Remote Similarity	NPC97614
0.5784	Remote Similarity	NPC262312
0.5784	Remote Similarity	NPC35269
0.5784	Remote Similarity	NPC23454
0.5784	Remote Similarity	NPC70323
0.5765	Remote Similarity	NPC476654
0.5765	Remote Similarity	NPC476657
0.5765	Remote Similarity	NPC476655
0.5747	Remote Similarity	NPC23721
0.5741	Remote Similarity	NPC477001
0.5741	Remote Similarity	NPC477000
0.5741	Remote Similarity	NPC74035
0.5714	Remote Similarity	NPC477421
0.5699	Remote Similarity	NPC11796
0.5699	Remote Similarity	NPC218817
0.5698	Remote Similarity	NPC476659
0.5698	Remote Similarity	NPC476656
0.5684	Remote Similarity	NPC82799
0.5682	Remote Similarity	NPC472947
0.5682	Remote Similarity	NPC473772
0.5679	Remote Similarity	NPC52012
0.5679	Remote Similarity	NPC474577
0.5676	Remote Similarity	NPC76976
0.5673	Remote Similarity	NPC45313
0.5673	Remote Similarity	NPC175614
0.5667	Remote Similarity	NPC55652
0.5667	Remote Similarity	NPC314678
0.5663	Remote Similarity	NPC81896
0.5663	Remote Similarity	NPC321919
0.5647	Remote Similarity	NPC476658
0.5647	Remote Similarity	NPC474928
0.5641	Remote Similarity	NPC49494
0.5641	Remote Similarity	NPC188341
0.5632	Remote Similarity	NPC473357
0.5632	Remote Similarity	NPC193029
0.5632	Remote Similarity	NPC470663
0.563	Remote Similarity	NPC478138
0.5625	Remote Similarity	NPC242930
0.5618	Remote Similarity	NPC315199
0.5618	Remote Similarity	NPC42526
0.5618	Remote Similarity	NPC129630
0.5604	Remote Similarity	NPC470992
0.5604	Remote Similarity	NPC474321
0.5604	Remote Similarity	NPC470993

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 NPC79367 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	61
0.1-0.2	830
0.2-0.3	5196
0.3-0.4	2527
0.4-0.5	496
0.5-0.6	37
0.6-0.7	3
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.7143	Intermediate Similarity	NPD3210	Clinical (unspecified phase)
0.6548	Remote Similarity	NPD3212	Clinical (unspecified phase)
0.6486	Remote Similarity	NPD3215	Phase 1
0.6216	Remote Similarity	NPD3214	Discontinued
0.6122	Remote Similarity	NPD8522	Clinical (unspecified phase)
0.587	Remote Similarity	NPD3732	Approved
0.5804	Remote Similarity	NPD6430	Approved
0.5804	Remote Similarity	NPD6429	Approved
0.5652	Remote Similarity	NPD818	Approved
0.5652	Remote Similarity	NPD819	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