Structure of PDB 4z2l Chain A Binding Site BS01

Receptor Information

>4z2l Chain A (length=498) Species: 615 (Serratia marcescens)

STRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSF
LDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSN
DLGVSHANYVNAVKTPAARTKFAQSCVRIMKDYGFDGVDIDWEYPQAAEV
DGFIAALQEIRTLLNQQTIADGRQALPYQLTIAGAGGAFFLSRYYSKLAQ
IVAPLDYINLMTYDLAGPWEKITNHQAALFGDAAGPTFYNALREANLGWS
WEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSG
GNGGQYSSHSTPGEDPYPNADYWLVGCDECVRDKDPRIASYRQLEQMLQG
NYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVM
FWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIM
TAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRLA

Ligand information

• Ligand ID: M6F
• InChI: InChI=1S/C31H55N5O10/c1-10-15-44-25-19(5)23(46-29(41)35-14-12-13-34-27(32)36-28(40)33-9)20(6)26(39)45-21(11-2)31(8,43)24(38)18(4)22(37)17(3)16-30(25,7)42/h1,17-25,37-38,42-43H,11-16H2,2-9H3,(H,35,41)(H4,32,33,34,36,40)/t17-,18+,19+,20-,21-,22+,23+,24-,25-,30-,31-/m1/s1
• InChIKey: BOCNNNRHDZJQLM-BKUHWZEQSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: CCC1C(C(C(C(C(CC(C(C(C(C(C(=O)O1)C)OC(=O)NCCCNC(=N)NC(=O)NC)C)OCC#C)(C)O)C)O)C)O)(C)O
  ACDLabs 12.01: N(C(=O)OC1C(C(=O)OC(CC)C(C)(O)C(O)C(C(O)C(C)CC(C(C1C)OCC#C)(O)C)C)C)CCCN\C(=N)NC(=O)NC
  CACTVS 3.385: CC[C@H]1OC(=O)[C@H](C)[C@@H](OC(=O)NCCCNC(=N)NC(=O)NC)[C@H](C)[C@@H](OCC#C)[C@](C)(O)C[C@@H](C)[C@H](O)[C@H](C)[C@@H](O)[C@]1(C)O
  OpenEye OEToolkits 1.9.2: [H]/N=C(\NCCCNC(=O)O[C@H]1[C@@H]([C@H]([C@](C[C@H]([C@@H]([C@@H]([C@H]([C@]([C@H](OC(=O)[C@@H]1C)CC)(C)O)O)C)O)C)(C)O)OCC#C)C)/NC(=O)NC
  CACTVS 3.385: CC[CH]1OC(=O)[CH](C)[CH](OC(=O)NCCCNC(=N)NC(=O)NC)[CH](C)[CH](OCC#C)[C](C)(O)C[CH](C)[CH](O)[CH](C)[CH](O)[C]1(C)O
• Formula: C31 H55 N5 O10
• Name: (3R,4S,5S,6R,7R,9R,10S,11S,12R,13S,14R)-14-ethyl-7,10,12,13-tetrahydroxy-3,5,7,9,11,13-hexamethyl-2-oxo-6-(prop-2-yn-1-yloxy)oxacyclotetradecan-4-yl {3-[N'-(methylcarbamoyl)carbamimidamido]propyl}carbamate
• ZINC: ZINC000263620281
• PDB chain: 4z2l Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4z2l Creation of Customized Bioactivity within a 14-Membered Macrolide Scaffold: Design, Synthesis, and Biological Evaluation Using a Family-18 Chitinase
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): Y10 F12 F51 D142 E144 M212 Y214 D215 Y292 D316 W403
• Binding residue (residue number reindexed from 1): Y9 F11 F50 D141 E143 M211 Y213 D214 Y291 D315 W402
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.85,IC50=1.41uM

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

External links

• PDB: RCSB:4z2l, PDBe:4z2l, PDBj:4z2l
• PDBsum: 4z2l
• PubMed: 26030312
• UniProt: P11797|CHIB_SERMA Chitinase B (Gene Name=chiB)