Structure of PDB 1p3d Chain A Binding Site BS02

Receptor Information
>1p3d Chain A (length=463) Species: 727 (Haemophilus influenzae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IIPEMRRVQQIHFIGIGGAGMSGIAEILLNEGYQISGSDIADGVVTQRLA
QAGAKIYIGHAEEHIEGASVVVVSSAIKDDNPELVTSKQKRIPVIQRAQM
LAEIMRFRHGIAVAGTHGKTTTTAMISMIYTQAKLDPTFVNGGLVKSAGK
NAHLGASRYLIAEADESDASFLHLQPMVSVVTNMEPDHMDTYEGDFEKMK
ATYVKFLHNLPFYGLAVMCADDPVLMELVPKVGRQVITYGFSEQADYRIE
DYEQTGFQGHYTVICPNNERINVLLNVPGKHNALNATAALAVAKEEGIAN
EAILEALADFQGAGRRFDQLGEFIRPNGKVRLVDDYGHHPTEVGVTIKAA
REGWGDKRIVMIFQPHRYSRTRDLFDDFVQVLSQVDALIMLDVYAAGEAP
IVGADSKSLCRSIRNLGKVDPILVSDTSQLGDVLDQIIQDGDLILAQGAG
SVSKISRGLAESW
Ligand information
Ligand IDUMA
InChIInChI=1S/C23H36N4O20P2/c1-8(21(35)36)24-19(34)9(2)43-18-14(25-10(3)29)22(45-11(6-28)16(18)32)46-49(40,41)47-48(38,39)42-7-12-15(31)17(33)20(44-12)27-5-4-13(30)26-23(27)37/h4-5,8-9,11-12,14-18,20,22,28,31-33H,6-7H2,1-3H3,(H,24,34)(H,25,29)(H,35,36)(H,38,39)(H,40,41)(H,26,30,37)/t8-,9+,11+,12+,14+,15+,16+,17+,18+,20+,22+/m0/s1
InChIKeyNTMMCWJNQNKACG-KBKUWGQMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C(=O)O)NC(=O)C(C)OC1C(C(OC(C1O)CO)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C
CACTVS 3.341C[CH](NC(=O)[CH](C)O[CH]1[CH](O)[CH](CO)O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH]1NC(C)=O)C(O)=O
OpenEye OEToolkits 1.5.0C[C@@H](C(=O)O)NC(=O)[C@@H](C)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)CO)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C
CACTVS 3.341C[C@H](NC(=O)[C@@H](C)O[C@H]1[C@H](O)[C@@H](CO)O[C@H](O[P@](O)(=O)O[P@@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@@H]1NC(C)=O)C(O)=O
ACDLabs 10.04O=P(OC1OC(C(O)C(OC(C(=O)NC(C(=O)O)C)C)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
FormulaC23 H36 N4 O20 P2
NameURIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE
ChEMBL
DrugBankDB01673
ZINCZINC000085545647
PDB chain1p3d Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1p3d Crystal Structures of Active Fully Assembled Substrate- and Product-Bound Complexes of UDP-N-Acetylmuramic Acid:L-Alanine Ligase (MurC) from Haemophilus influenzae.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G25 G28 A29 G30 M31 D49 I50 H70 S84 A86 I87 R107 D175 H348 H376 R377 R380
Binding residue
(residue number reindexed from 1)		G15 G18 A19 G20 M21 D39 I40 H60 S74 A76 I77 R97 D165 H338 H366 R367 R370
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) K129 T130 L154 E173 H198
Catalytic site (residue number reindexed from 1) K119 T120 L144 E163 H188
Enzyme Commision number 6.3.2.8: UDP-N-acetylmuramate--L-alanine ligase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008763 UDP-N-acetylmuramate-L-alanine ligase activity
GO:0016874 ligase activity
GO:0016881 acid-amino acid ligase activity
Biological Process
GO:0008360 regulation of cell shape
GO:0009058 biosynthetic process
GO:0009252 peptidoglycan biosynthetic process
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1p3d, PDBe:1p3d, PDBj:1p3d
PDBsum1p3d
PubMed12837790
UniProtP45066|MURC_HAEIN UDP-N-acetylmuramate--L-alanine ligase (Gene Name=murC)

[Back to BioLiP]