NPASS Compound

Natural Product: NPC100321

Natural Product ID	NPC100321
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Chrysaibol
IUPAC Name	(2S)-2-[[(2S)-1-[2-[[(2S)-2-[[(2S)-2-[[2-[[2-[[2-[[(2S)-2-[[(2S)-2-[[(2S)-2-[[2-[[2-[[(2S)-2-acetamido-3-(1H-indol-3-yl)propanoyl]amino]-2-methylpropanoyl]amino]-2-methylpropanoyl]amino]-4-methylpentanoyl]amino]-3-methylbutanoyl]amino]-5-amino-5-oxopentanoyl]amino]-2-methylpropanoyl]amino]-2-methylpropanoyl]amino]-2-methylpropanoyl]amino]-5-amino-5-oxopentanoyl]amino]-4-methylpentanoyl]amino]-2-methylpropanoyl]pyrrolidine-2-carbonyl]amino]-N-[(2S)-1-hydroxypropan-2-yl]pentanediamide
Synonyms	chrysaibol
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL504009
PubChem CID	25058082
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0003297] Organic Polymers [CHEMONTID:0003298] Polypeptides

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 2D 240242 0 0 0 0 0 0 0 0999 V2000 -2.3268 16.0989 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6971 16.7090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0674 17.3191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4573 18.6895 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2.9655 18.8462 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3554 20.2166 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9851 19.6065 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.8283 18.1147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5420 17.5046 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2080 16.2055 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7957 15.0908 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1660 15.7009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0093 17.1927 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.1240 18.1964 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8121 19.6636 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5506 17.7329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0141 19.1595 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.4813 19.4713 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9448 20.8979 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3714 20.4344 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 8.6833 18.9672 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.1099 18.5036 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6463 17.0771 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 8.1791 16.7652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7156 15.3386 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.1422 14.8751 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 9.4540 13.4079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.8806 12.9443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.4171 11.5177 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 8.9499 11.2059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.4864 9.7793 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0598 10.2428 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 5.9451 9.2391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2569 7.7719 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7897 7.4600 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 4.3262 6.0335 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8590 5.7216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3917 5.4097 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0755 5.0978 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0799 6.8769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1708 4.2544 0.0000 N 0 0 0 0 0 0 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40136 1 0 40137 1 0 40138 1 0 43139 1 1 52140 1 1 53141 1 0 53142 1 0 55143 1 0 56144 1 0 59145 1 0 60146 1 0 61147 1 0 62148 1 0 65149 1 0 66150 1 0 66151 1 0 66152 1 0 67153 1 0 68154 1 0 68155 1 0 68156 1 0 69157 1 0 69158 1 0 69159 1 0 70160 1 0 71161 1 0 71162 1 0 71163 1 0 72164 1 0 72165 1 0 72166 1 0 73167 1 0 74168 1 0 74169 1 0 75170 1 0 76171 1 0 76172 1 0 76173 1 0 77174 1 0 77175 1 0 77176 1 0 78177 1 0 79178 1 0 80179 1 0 80180 1 0 81181 1 0 81182 1 0 83183 1 0 84184 1 0 85185 1 0 86186 1 0 86187 1 0 86188 1 0 87189 1 0 87190 1 0 87191 1 0 88192 1 0 89193 1 0 89194 1 0 89195 1 0 90196 1 0 90197 1 0 90198 1 0 91199 1 0 92200 1 0 92201 1 0 92202 1 0 93203 1 0 93204 1 0 93205 1 0 94206 1 0 95207 1 0 95208 1 0 96209 1 0 96210 1 0 98211 1 0 99212 1 0 100213 1 0 101214 1 0 101215 1 0 102216 1 0 103217 1 0 103218 1 0 103219 1 0 104220 1 0 104221 1 0 104222 1 0 105223 1 0 106224 1 0 106225 1 0 106226 1 0 107227 1 0 107228 1 0 107229 1 0 108230 1 0 109231 1 0 109232 1 0 110233 1 0 110234 1 0 112235 1 0 113236 1 0 114237 1 0 115238 1 0 115239 1 0 115240 1 0 M END

Standard InCHIKey	IPCNUNZLKUHWAZ-WGRFOCSXSA-N
Standard InCHI	InChI=1S/C77H125N19O19/c1-39(2)34-50(88-67(111)73(11,12)93-68(112)75(15,16)91-63(107)52(83-43(8)98)36-44-37-81-46-25-22-21-24-45(44)46)60(104)89-57(41(5)6)65(109)85-49(29-32-56(80)101)61(105)90-74(13,14)69(113)95-76(17,18)70(114)94-72(9,10)66(110)87-48(28-31-55(79)100)59(103)86-51(35-40(3)4)62(106)92-77(19,20)71(115)96-33-23-26-53(96)64(108)84-47(27-30-54(78)99)58(102)82-42(7)38-97/h21-22,24-25,37,39-42,47-53,57,81,97H,23,26-36,38H2,1-20H3,(H2,78,99)(H2,79,100)(H2,80,101)(H,82,102)(H,83,98)(H,84,108)(H,85,109)(H,86,103)(H,87,110)(H,88,111)(H,89,104)(H,90,105)(H,91,107)(H,92,106)(H,93,112)(H,94,114)(H,95,113)/t42-,47-,48-,49-,50-,51-,52-,53-,57-/m0/s1
SMILES	OC[C@@H](N=C([C@@H](N=C([C@@H]1CCCN1C(=O)C(N=C([C@@H](N=C([C@@H](N=C(C(N=C(C(N=C(C(N=C([C@@H](N=C([C@H](C(C)C)N=C([C@@H](N=C(C(N=C(C(N=C([C@H](Cc1c[nH]c2c1cccc2)N=C(O)C)O)(C)C)O)(C)C)O)CC(C)C)O)O)CCC(=N)O)O)(C)C)O)(C)C)O)(C)C)O)CCC(=N)O)O)CC(C)C)O)(C)C)O)CCC(=N)O)O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	1619.94	Volume:	1632.629 ? Van der Waals volume.
Dense:	0.992	LogP:	4.909 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.703 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-2.918 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	46.0	Rigid Bonds:	33.0
TPSA:	644.83 ? Topological Polar Surface Area.	H-Bond Acceptor:	38.0
H-Bond Donor:	22.0	Rings:	3.0
Heavy Atoms:	38.0

MedChem Properties

QED Drug-Likeness Score:	0.022	GASA:	1.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	7.31	Fsp³:	0.662
MCE-18:	186.812 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Accepted	BMS Rule:	1
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.333	Fluc inhibitor:	0.0 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.444 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.683 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.063	Promiscuous compounds:	0.251

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-6.525	MDCK Permeability:	-5.012
Pgp-inhibitor:	0.0	Pgp-substrate:	1.0
PAMPA:	1.0 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.905
20% Bioavailability (F20%):	1.0	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.977
Plasma Protein Binding (PPB):	73.656%	Volume Distribution (VD):	-0.133
Fu:	28.828% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	1.0
OATP1B3 inhibitor:	1.0	BCRP inhibitor:	0.0
BSEP inhibitor:	0.258

ADMET: Metabolism

CYP1A2-inhibitor:	0.0	CYP1A2-substrate:	0.0
CYP2C19-inhibitor:	1.0	CYP2C19-substrate:	0.0
CYP2C9-inhibitor:	1.0	CYP2C9-substrate:	0.0
CYP2D6-inhibitor:	0.0	CYP2D6-substrate:	0.0
CYP3A4-inhibitor:	1.0	CYP3A4-substrate:	0.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	0.0
HLM stability:	0.023 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

-1.164

Half-life (T1/2):

5.378

ADMET: Toxicity

hERG Blockers:	0.0	hERG Blockers (10um):	0.0
Human Hepatotoxicity (H-HT):	1.0	Drug-induced Liver Injury (DILI):	1.0
AMES Toxicity:	0.974	Rat Oral Acute Toxicity:	0.978
Maximum Recommended Daily Dose:	0.319	Skin Sensitization:	1.0
Carcinogencity:	1.0	Eye Corrosion:	0.0
Eye Irritation:	0.0	Respiratory Toxicity:	0.99
Drug-induced Neurotoxicity:	0.0	Ototoxicity:	1.0
Hematotoxicity:	0.061	Drug-induced Nephrotoxicity:	1.0
Genotoxicity:	1.0	RPMI-8226 Immunitoxicity:	0.0
A549 Cytotoxicity:	0.0	Hek293 Cytotoxicity:	0.0
BCF:	-0.27 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	2.847 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	4.841 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	3.862 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO33104	sepedonium chrysospermum	Species	Hypocreaceae	Eukaryota	n.a.	New Zealand	n.a.	PMID[17067166]
NPO33104	sepedonium chrysospermum	Species	Hypocreaceae	Eukaryota	n.a.	New Zealand	n.a.	PMID[18702471]

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	Organism Name	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	1
Organism	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT168	Cell line	P388	Mus musculus	IC50	=	6610.0	nM	PMID[19182783]
NPT79	Organism	Bacillus subtilis	Bacillus subtilis	IC50	=	1540.0	nM	PMID[19182783]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC100321 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	25364
0.1-0.2	22926
0.2-0.3	1223
0.3-0.4	251
0.4-0.5	48
0.5-0.6	34
0.6-0.7	2
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	Natural Product ID
0.7739	Intermediate Similarity	NPC486282
0.712	Intermediate Similarity	NPC486283
0.6132	Remote Similarity	NPC479362
0.6038	Remote Similarity	NPC479364
0.5785	Remote Similarity	NPC486280
0.5776	Remote Similarity	NPC31385
0.5738	Remote Similarity	NPC486278
0.5736	Remote Similarity	NPC479574
0.5702	Remote Similarity	NPC107077
0.569	Remote Similarity	NPC223791
0.5678	Remote Similarity	NPC110602
0.5678	Remote Similarity	NPC479071
0.5645	Remote Similarity	NPC486275
0.5636	Remote Similarity	NPC479361
0.5556	Remote Similarity	NPC486273
0.5545	Remote Similarity	NPC479365
0.5545	Remote Similarity	NPC479363
0.5538	Remote Similarity	NPC325976
0.5538	Remote Similarity	NPC326363
0.5536	Remote Similarity	NPC489625
0.5478	Remote Similarity	NPC293917
0.5476	Remote Similarity	NPC486281
0.5433	Remote Similarity	NPC486279
0.5403	Remote Similarity	NPC479076
0.5328	Remote Similarity	NPC479075
0.5323	Remote Similarity	NPC479073
0.5317	Remote Similarity	NPC75726
0.5303	Remote Similarity	NPC486271
0.5299	Remote Similarity	NPC483341
0.5242	Remote Similarity	NPC479065
0.5238	Remote Similarity	NPC479066
0.5203	Remote Similarity	NPC155143
0.5161	Remote Similarity	NPC320968
0.5075	Remote Similarity	NPC141050
0.5072	Remote Similarity	NPC486274
0.5041	Remote Similarity	NPC54420
0.5038	Remote Similarity	NPC483985
0.5036	Remote Similarity	NPC486272

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC100321 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4441
0.1-0.2	4491
0.2-0.3	186
0.3-0.4	26
0.4-0.5	5
0.5-0.6	1
0.6-0.7	0
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
0.5478	Remote Similarity	NPD7621	Clinical (unspecified phase)

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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