Structure of PDB 3t8w Chain B Binding Site BS04

Receptor Information
>3t8w Chain B (length=517) Species: 36329 (Plasmodium falciparum 3D7) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SEVPQVVSLDPTSIPIEYNTPIHDIKVQVYDIKGGCNVEEGLTIFLVNNP
GKENGPVKISSKVNDKQVSEFLKDENMEKFNVKLGTSKHFYMFNDNKNSV
AVGYVGCGSVADLSEADMKRVVLSLVTMLHDNKLSKLTVVFEINVDKNLF
RFFLETLFYEYMTDERFKSTKNVNMEYIKHLGVYINNADTYKEEVEKARV
YYFGTYYASQLIAAPSNYCNPVSLSNAAVELAQKLNLEYKILGVKELEEL
KMGAYLSVGKGSMYPNKFIHLTYKSKGDVKKKIALVGKGITFDSGGYNLK
AAPGSMIDLMKFDMSGCAAVLGCAYCVGTLKPENVEIHFLSAVCENMVSK
NSYRPGDIITASNGKTIEVGNTDAEGRLTLADALVYAEKLGVDYIVDIAT
LTGAMLYSLGTSYAGVFGNNEELINKILQSSKTSNEPVWWLPIINEYRAT
LNSKYADINQISSSVKASSIVASLFLKEFVQNTAWAHIDIAGVSWNFKAR
KPKGFGVRLLTEFVLND
Ligand information
Ligand IDDGZ
InChIInChI=1S/C57H67N7O10/c1-2-3-6-22-50(65)60-29-14-13-21-47(54(59)69)63-56(71)49(36-40-23-27-44(28-24-40)52(67)43-18-9-5-10-19-43)62-51(66)38-74-33-32-73-31-30-61-55(70)48(37-41-25-26-42-17-11-12-20-45(42)34-41)64-57(72)53(68)46(58)35-39-15-7-4-8-16-39/h1,4-5,7-12,15-20,23-28,34,46-49,53,68H,3,6,13-14,21-22,29-33,35-38,58H2,(H2,59,69)(H,60,65)(H,61,70)(H,62,66)(H,63,71)(H,64,72)/t46-,47+,48+,49+,53+/m1/s1
InChIKeyDTRONJOHRJXFLK-VGMISYGZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2C#CCCCC(=O)NCCCC[C@@H](C(=O)N)NC(=O)[C@H](Cc1ccc(cc1)C(=O)c2ccccc2)NC(=O)COCCOCCNC(=O)[C@H](Cc3ccc4ccccc4c3)NC(=O)[C@H]([C@@H](Cc5ccccc5)N)O
OpenEye OEToolkits 1.7.2C#CCCCC(=O)NCCCCC(C(=O)N)NC(=O)C(Cc1ccc(cc1)C(=O)c2ccccc2)NC(=O)COCCOCCNC(=O)C(Cc3ccc4ccccc4c3)NC(=O)C(C(Cc5ccccc5)N)O
CACTVS 3.370N[CH](Cc1ccccc1)[CH](O)C(=O)N[CH](Cc2ccc3ccccc3c2)C(=O)NCCOCCOCC(=O)N[CH](Cc4ccc(cc4)C(=O)c5ccccc5)C(=O)N[CH](CCCCNC(=O)CCCC#C)C(N)=O
CACTVS 3.370N[C@H](Cc1ccccc1)[C@H](O)C(=O)N[C@@H](Cc2ccc3ccccc3c2)C(=O)NCCOCCOCC(=O)N[C@@H](Cc4ccc(cc4)C(=O)c5ccccc5)C(=O)N[C@@H](CCCCNC(=O)CCCC#C)C(N)=O
ACDLabs 12.01O=C(N)C(NC(=O)C(NC(=O)COCCOCCNC(=O)C(NC(=O)C(O)C(N)Cc1ccccc1)Cc3cc2ccccc2cc3)Cc4ccc(cc4)C(=O)c5ccccc5)CCCCNC(=O)CCCC#C
FormulaC57 H67 N7 O10
NameN-((2R,3S,6S,18S,21S)-2-amino-18-(4-benzoylbenzyl)-21-carbamoyl-3-hydroxy-6-(naphthalen-2-ylmethyl)-4,7,16,19-tetraoxo-1-phenyl-11,14-dioxa-5,8,17,20-tetraazapentacosan-25-yl)hex-5-ynamide
ChEMBL
DrugBank
ZINC
PDB chain3t8w Chain B Residue 615 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3t8w Bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases
Resolution2.0 Å
Binding residue
(original residue number in PDB)		K374 D379 A388 P389 G390 M392 M396 F398 D399 N457 D459 E461 T486 L487 G489 A490 Y493 I547
Binding residue
(residue number reindexed from 1)		K288 D293 A302 P303 G304 M306 M310 F312 D313 N371 D373 E375 T400 L401 G403 A404 Y407 I461
Annotation score1
Binding affinityMOAD: Ki=330nM
PDBbind-CN: -logKd/Ki=7.54,Ki=29nM
Enzymatic activity
Catalytic site (original residue number in PDB) K386 R463
Catalytic site (residue number reindexed from 1) K300 R377
Enzyme Commision number 3.4.11.1: leucyl aminopeptidase.
3.4.13.-
Gene Ontology
Molecular Function
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
GO:0070006 metalloaminopeptidase activity
Biological Process
GO:0006508 proteolysis
GO:0019538 protein metabolic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3t8w, PDBe:3t8w, PDBj:3t8w
PDBsum3t8w
PubMed21844374
UniProtQ8IL11|AMPL_PLAF7 Leucine aminopeptidase (Gene Name=LAP)

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