Structure of PDB 3wd4 Chain A Binding Site BS01

Receptor Information
>3wd4 Chain A (length=497) Species: 615 (Serratia marcescens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
STRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSF
LDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSN
DLGVSHANYVNAVKTPAARTKFAQSCVRIMKDYGFDGVDIDWEYPQAAEV
DGFIAALQEIRTLLNQQTIADGRQALPYQLTIAGAGGAFFLSRYYSKLAQ
IVAPLDYINLMTYDLAGPWEKITNHQAALFGDAAGPTFYNALREANLGWS
WEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSG
GNGGQYSSHSTPGEDPYPNADYWLVGCDECVRDKDPRIASYRQLEQMLQG
NYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVM
FWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIM
TAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRL
Ligand information
Ligand IDA1L
InChIInChI=1S/C24H31N9O3/c1-27-24(36)31-23(25)28-14-8-13-20(30-21(34)15-29-32-26)22(35)33(16-18-9-4-2-5-10-18)17-19-11-6-3-7-12-19/h2-7,9-12,20H,8,13-17H2,1H3,(H,30,34)(H4,25,27,28,31,36)/t20-/m0/s1
InChIKeyWCLXSHAWFUUDKF-FQEVSTJZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CNC(=O)NC(=N)NCCCC(C(=O)N(Cc1ccccc1)Cc2ccccc2)NC(=O)C[N-][N+]#N
OpenEye OEToolkits 1.7.6[H]/N=C(\NCCC[C@@H](C(=O)N(Cc1ccccc1)Cc2ccccc2)NC(=O)C[N-][N+]#N)/NC(=O)NC
CACTVS 3.385CNC(=O)NC(=N)NCCC[C@H](NC(=O)C[N-][N+]#N)C(=O)N(Cc1ccccc1)Cc2ccccc2
CACTVS 3.385CNC(=O)NC(=N)NCCC[CH](NC(=O)C[N-][N+]#N)C(=O)N(Cc1ccccc1)Cc2ccccc2
ACDLabs 12.01N#[N+][N-]CC(=O)NC(C(=O)N(Cc1ccccc1)Cc2ccccc2)CCCNC(=[N@H])NC(=O)NC
FormulaC24 H31 N9 O3
Name[2-[[(2S)-1-[bis(phenylmethyl)amino]-5-[[N-(methylcarbamoyl)carbamimidoyl]amino]-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-diazonio-azanide
ChEMBLCHEMBL4754642
DrugBank
ZINCZINC000140068785
PDB chain3wd4 Chain A Residue 511 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3wd4 Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor
Resolution2.0 Å
Binding residue
(original residue number in PDB)
Y10 F12 W97 D142 E144 M212 Y214 D215 Y292 R294 R338 W403
Binding residue
(residue number reindexed from 1)
Y9 F11 W96 D141 E143 M211 Y213 D214 Y291 R293 R337 W402
Annotation score1
Binding affinityMOAD: ic50=0.58uM
Enzymatic activity
Catalytic site (original residue number in PDB) D140 D142 E144 Y214
Catalytic site (residue number reindexed from 1) D139 D141 E143 Y213
Enzyme Commision number 3.2.1.14: chitinase.
Gene Ontology
Molecular Function
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0008061 chitin binding
GO:0030246 carbohydrate binding
Biological Process
GO:0005975 carbohydrate metabolic process
Cellular Component
GO:0005576 extracellular region

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:3wd4, PDBe:3wd4, PDBj:3wd4
PDBsum3wd4
PubMed24043811
UniProtP11797|CHIB_SERMA Chitinase B (Gene Name=chiB)

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