Structure of PDB 4d9p Chain A Binding Site BS01

Receptor Information
>4d9p Chain A (length=264) Species: 191218 (Bacillus anthracis str. A2012) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KWDYDLRCGEYTLNLNEKTLIMGILNVTPDSFSDGGSYNEVDAAVRHAKE
MRDEGAHIIDIGGVSVEEEIKRVVPMIQAVSKEVKLPISIDTYKAEVAKQ
AIEAGAHIINDIWGAKAEPKIAEVAAHYDVPIILMHNRDNMNYRNLMADM
IADLYDSIKIAKDAGVRDENIILDPGIGFAKTPEQNLEAMRNLEQLNVLG
YPVLLGTSRKSFIGHVLDLPVEERLEGTGATVCLGIEKGCEFVRVHDVKE
MSRMAKMMDAMIGK
Ligand information
Ligand IDZ17
InChIInChI=1S/C11H13N5O4/c1-4(3-5(17)18)7-8(19)6-9(16(2)15-7)13-11(12)14-10(6)20/h4H,3H2,1-2H3,(H,17,18)(H3,12,13,14,20)/t4-/m1/s1
InChIKeySXWJQNIIWHUAJQ-SCSAIBSYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)CC(C1=NN(C=2N=C(NC(=O)C=2C1=O)N)C)C
CACTVS 3.370C[CH](CC(O)=O)C1=NN(C)C2=C(C(=O)NC(=N2)N)C1=O
OpenEye OEToolkits 1.7.6CC(CC(=O)O)C1=NN(C2=C(C1=O)C(=O)NC(=N2)N)C
OpenEye OEToolkits 1.7.6C[C@H](CC(=O)O)C1=NN(C2=C(C1=O)C(=O)NC(=N2)N)C
CACTVS 3.370C[C@H](CC(O)=O)C1=NN(C)C2=C(C(=O)NC(=N2)N)C1=O
FormulaC11 H13 N5 O4
Name(3R)-3-(7-amino-1-methyl-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)butanoic acid
ChEMBL
DrugBank
ZINCZINC000095920570
PDB chain4d9p Chain A Residue 306 [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]
PDB4d9p Structure-Based Design of Novel Pyrimido[4,5-c]pyridazine Derivatives as Dihydropteroate Synthase Inhibitors with Increased Affinity.
Resolution2.26 Å
Binding residue
(original residue number in PDB)		D101 N120 I122 M145 D184 F189 G216 K220 R254
Binding residue
(residue number reindexed from 1)		D91 N110 I112 M135 D174 F179 G206 K210 R244
Annotation score1
Binding affinityMOAD: ic50=145uM
PDBbind-CN: -logKd/Ki=3.84,IC50=145uM
Enzymatic activity
Catalytic site (original residue number in PDB) V28 D54 K220 R254
Catalytic site (residue number reindexed from 1) V27 D53 K210 R244
Enzyme Commision number 2.5.1.15: dihydropteroate synthase.
Gene Ontology
Molecular Function
GO:0004156 dihydropteroate synthase activity
GO:0016740 transferase activity
GO:0046872 metal ion binding
Biological Process
GO:0009396 folic acid-containing compound biosynthetic process
GO:0042558 pteridine-containing compound metabolic process
GO:0044237 cellular metabolic process
GO:0046654 tetrahydrofolate biosynthetic process
GO:0046656 folic acid biosynthetic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4d9p, PDBe:4d9p, PDBj:4d9p
PDBsum4d9p
PubMed22416048
UniProtQ81VW8

[Back to BioLiP]