Structure of PDB 2zlg Chain A Binding Site BS01

Receptor Information

>2zlg Chain A (length=654) Species: 4932 (Saccharomyces cerevisiae)

TLAARIAISNLHKQTTKQFSKVVEDLYRYVNAATGKPAPMISDDVYNIVM
ENKDKLNSAIVYDRDFQYSYFGFKTLERSYLLRINGQVAERPQHLIMRVA
LGIHGRDIEAALETYNLMSLKYFTHASPTLFNAGTPKPQMSSCFLVAMKE
DSIEGIYDTLKECALISKTAGGIGLHIHNIRSTGSYIAGTNGTSNGLIPM
IRVFNNTARYVGAFALYLEPWHADIFDFIDIRKNHGKEEIRARDLFPALW
IPDLFMKRVEENGTWTLFSPTSAPGLSDCYGDEFEALYTRYEKEGRGKTI
KAQKLWYSILEAQTETGTPFVVYKDACNRKSNQKNLGVIKSSNLCCEIVE
YSAPDETAVCNLASVALPAFIETSEDGKTSTYNFKKLHEIAKVVTRNLNR
VIDRNYYPVEEARKSNMRHRPIALGVQGLADTFMLLRLPFDSEEARLLNI
QIFETIYHASMEASCELAQKDGPYETFQGSPASQGILQFDMWDQKPYGMW
DWDTLRKDIMKHGVRNSLTMAPMPTASTSQILGYNECFEPVTSNMFQVVN
PYLLRDLVDLGIWDEGMKQYLITQNGSIQGLPNVPQELKDLYKTVWEISQ
KTIINMAADRSVYIDQSHSLNLFLRAPTMGKLTSMHFYGWKKGLKTGMYY
LRTQ

Ligand information

• Ligand ID: MRT
• InChI: InChI=1S/C56H66N6O13/c1-33(2)27-42(57-31-46(63)50(36-21-11-6-12-22-36)62(3)56(74)75-32-41-39-25-15-13-23-37(39)38-24-14-16-26-40(38)41)51(68)58-44(30-48(66)67)53(70)61-49(35-19-9-5-10-20-35)54(71)59-43(29-47(64)65)52(69)60-45(55(72)73)28-34-17-7-4-8-18-34/h4,6-8,11-18,21-26,33,35,41-45,49-50,57H,5,9-10,19-20,27-32H2,1-3H3,(H,58,68)(H,59,71)(H,60,69)(H,61,70)(H,64,65)(H,66,67)(H,72,73)/t42-,43-,44-,45-,49-,50+/m0/s1
• InChIKey: VHDDRUTXAIHKQU-NXKHAHLZSA-N
• SMILES:
  ACDLabs 10.04: O=C(OCC3c1ccccc1c2ccccc23)N(C)C(c4ccccc4)C(=O)CNC(C(=O)NC(C(=O)NC(C(=O)NC(C(=O)NC(C(=O)O)Cc5ccccc5)CC(=O)O)C6CCCCC6)CC(=O)O)CC(C)C
  OpenEye OEToolkits 1.5.0: CC(C)CC(C(=O)NC(CC(=O)O)C(=O)NC(C1CCCCC1)C(=O)NC(CC(=O)O)C(=O)NC(Cc2ccccc2)C(=O)O)NCC(=O)C(c3ccccc3)N(C)C(=O)OCC4c5ccccc5-c6c4cccc6
  CACTVS 3.341: CC(C)C[CH](NCC(=O)[CH](N(C)C(=O)OCC1c2ccccc2c3ccccc13)c4ccccc4)C(=O)N[CH](CC(O)=O)C(=O)N[CH](C5CCCCC5)C(=O)N[CH](CC(O)=O)C(=O)N[CH](Cc6ccccc6)C(O)=O
  OpenEye OEToolkits 1.5.0: CC(C)C[C@@H](C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](C1CCCCC1)C(=O)N[C@@H](CC(=O)O)C(=O)N[C@@H](Cc2ccccc2)C(=O)O)NCC(=O)[C@@H](c3ccccc3)N(C)C(=O)OCC4c5ccccc5-c6c4cccc6
  CACTVS 3.341: CC(C)C[C@H](NCC(=O)[C@H](N(C)C(=O)OCC1c2ccccc2c3ccccc13)c4ccccc4)C(=O)N[C@@H](CC(O)=O)C(=O)N[C@@H](C5CCCCC5)C(=O)N[C@@H](CC(O)=O)C(=O)N[C@@H](Cc6ccccc6)C(O)=O
• Formula: C56 H66 N6 O13
• Name: (5R,9S,12S,15S,18S,21S)-21-benzyl-12,18-bis(carboxymethyl)-15-cyclohexyl-1-(9H-fluoren-9-yl)-4-methyl-9-(2-methylpropyl)-3,6,10,13,16,19-hexaoxo-5-phenyl-2-oxa-4,8,11,14,17,20-hexaazadocosan-22-oic acid
• PDB chain: 2zlg Chain A Residue 889

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2zlg The Structural Basis for Peptidomimetic Inhibition of Eukaryotic Ribonucleotide Reductase: A Conformationally Flexible Pharmacophore
• Resolution: 2.52 Å
• Binding residue (original residue number in PDB): Q692 K693 M721 S726 Y730
• Binding residue (residue number reindexed from 1): Q600 K601 M629 S634 Y638
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.59,IC50=2.6uM

Enzymatic activity

• Catalytic site (original residue number in PDB): C218 N426 C428 E430 C443 Y741 Y742
• Catalytic site (residue number reindexed from 1): C143 N343 C345 E347 C360 Y649 Y650
• Enzyme Commision number: 1.17.4.1: ribonucleoside-diphosphate reductase.

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0016491 oxidoreductase activity
• GO:0042802 identical protein binding

Biological Process

• GO:0009263 deoxyribonucleotide biosynthetic process

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005971 ribonucleoside-diphosphate reductase complex

External links

• PDB: RCSB:2zlg, PDBe:2zlg, PDBj:2zlg
• PDBsum: 2zlg
• PubMed: 18610997
• UniProt: P21524|RIR1_YEAST Ribonucleoside-diphosphate reductase large chain 1 (Gene Name=RNR1)