Ligands, dictionary and refinement

Garib N MurshudovYork Structural Biology Laboratory

University of York

Outline

1. Introduction2. Dictionary of ligands3. Sources of dictionary and idealised coordinates4. Tools for ligand description in ccp45. How to use dictionary in refinement (REFMAC)6. Conclusions

The need for prior chemical knowledge

• Refinement• Atomic model description

GraphicsSimulations………..

Atomic model description

. . . . . .ATOM 7 C LEU A 5 37.584 4.085 ATOM 8 O LEU A 5 36.548 3.447 ATOM 9 N ILE A 6 37.887 5.098 ATOM 10 CA ILE A 6 37.032 5.447 ATOM 11 CB ILE A 6 37.835 6.276 . . . . . .

Default pointers in PDB file

Pointer to link description

Pointer to monomer description

Pointer to atom description

Refmac5 Dictionary

• Describes all amino acids• All nucleic acids• Common sugars• Many organic and inorganic

compounds• Links and modifications

There are tools to deal with dictionary Dictionary format is mmCIF

atoms

bonds

angles

torsions

chiralities

planes

tree

list of monomers

bonds

angles

torsions

chiralities

planes

tree

list of links

atoms

bonds

angles

torsions

chiralities

planes

tree

list of modifications

types

bonds

angles

VDW

H-bonds

list ofatom types

dictionary

General categorydata_comp_listloop__chem_comp.id_chem_comp.three_letter_code_chem_comp.name_chem_comp.group_chem_comp.number_atoms_all_chem_comp.number_atoms_nh_chem_comp.desc_level. . . . . . . . .

GLC-b-D GLC 'beta_D_glucose ' D-pyranose 24 12 .

Group: peptide, DNA/RNA, pyranose, non-polymerLevel: C or M – complete or minimal description

Atom categoryloop__chem_comp_atom.comp_id_chem_comp_atom.atom_id_chem_comp_atom.type_symbol_chem_comp_atom.type_energy_chem_comp_atom.partial_charge_chem_comp_atom.x_chem_comp_atom.y_chem_comp_atom.z GLC-b-D C1 C CH1 0 0.0 0.0 0.0 GLC-b-D H1 H HCH1 0 0.522 -0.087 0.801 . . . . .

Bond categoryloop__chem_comp_bond.comp_id_chem_comp_bond.atom_id_1_chem_comp_bond.atom_id_2_chem_comp_bond.type_chem_comp_bond.value_dist_chem_comp_bond.value_dist_esd GLC-b-D O1 C1 single 1.410 0.020 GLC-b-D C2 C1 single 1.524 0.020 . . . . .

Type: single, double, triple, aromatic, metal

Angle categoryloop__chem_comp_angle.comp_id_chem_comp_angle.atom_id_1_chem_comp_angle.atom_id_2_chem_comp_angle.atom_id_3_chem_comp_angle.value_angle_chem_comp_angle.value_angle_esd GLC-b-D H1 C1 O1 109.470 3.000 GLC-b-D O1 C1 C2 109.470 3.000. . . . . .

Torsion angles categoryloop_

_chem_comp_tor.comp_id_chem_comp_tor.id_chem_comp_tor.atom_id_1_chem_comp_tor.atom_id_2_chem_comp_tor.atom_id_3_chem_comp_tor.atom_id_4_chem_comp_tor.value_angle_chem_comp_tor.value_angle_esd_chem_comp_tor.period GLC-b-D var_1 C1 C2 O2 HO2 0.000 20.000 1 GLC-b-D var_2 C1 C2 C3 C4 -50.095 20.000 3. . . . . .

Period: number of energetic minima

1

2 3

4

Chirality category

1.Tetrahedral chirality

2.Non-tetrahedral chirality

Usually on C or N with sp3 hybridisation

Usually for metalcoordination

Chirality categoryloop__chem_comp_chir.comp_id_chem_comp_chir.id_chem_comp_chir.atom_id_centre_chem_comp_chir.atom_id_1_chem_comp_chir.atom_id_2_chem_comp_chir.atom_id_3_chem_comp_chir.volume_signGLC-b-D chir_01 C5 C4 O5 C6 positiveGLC-b-D chir_02 C4 C3 O4 C5 positive GLC-b-D chir_03 C3 C2 O3 C4 negative GLC-b-D chir_04 C2 C1 O2 C3 positive . . . . .

Sign: positive, negative, both, anomer

1 3C

+_

Metal chiralityMetal chirality is only used to create coordinatesloop__chem_comp_chir.comp_id_chem_comp_chir.id_chem_comp_chir.atom_id_centre_chem_comp_chir.atom_id_1_chem_comp_chir.atom_id_2. . . . _chem_comp_chir.atom_id_8_chem_comp_chir.volume_signMONid chir_id Ac Ab Af A1 A2 A3 A4 A5 A6 cross6

Where: Ac - chiral centre atom Ab - back atom,Af - forward atom A1,A2,...,AN - atoms in the same plane, N can be = 0,1,2,3,4,5,6 these atoms form the point group. crossN - cross chirality specification

Example metal chirality (OC7)

OC7 chir_01 CA O5 O7 O1 O4 O2 O3 O6 . cross5

CAO5 O7

O1

O4

O2O3

O6

Plane categoryloop__chem_comp_plane_atom.comp_id_chem_comp_plane_atom.plane_id_chem_comp_plane_atom.atom_id_chem_comp_plane_atom.dist_esd PHE plan CB 0.020 PHE plan CG 0.020 PHE plan CD1 0.020 . . . . .

Example of a modification

CH2OHH

NH3+

O

O O

P

O

O O

3-

CH2H

NH3+

O

O

O

PO

OO

2-

+

OH-

Modification formalism allows to change a monomer

Modification describes in details the result of chemical reaction

Modification: general category

data_mod_listloop__chem_mod.id_chem_mod.name_chem_mod.comp_id_chem_mod.group_id. . . . . . O1MET O1_metyl_of_sugar . pyranose

group_id: means only for sugars

Modification: atom category

loop__chem_mod_atom.mod_id_chem_mod_atom.function_chem_mod_atom.atom_id_chem_mod_atom.new_atom_id_chem_mod_atom.new_type_symbol_chem_mod_atom.new_type_energy_chem_mod_atom.new_partial_charge O1MET change O1 . . O2 0.000 O1MET delete HO1 . . . 0.000 O1MET add . CM C CH3 0.000 O1MET add . HM1 H HCH 0.000 . . . . . .

function: only - change, delete or add

Modification: bond category

loop__chem_mod_bond.mod_id_chem_mod_bond.function_chem_mod_bond.atom_id_1_chem_mod_bond.atom_id_2_chem_mod_bond.new_type_chem_mod_bond.new_value_dist_chem_mod_bond.new_value_dist_esd O1MET add O1 CM single 1.420 0.020 O1MET add CM HM1 single 0.960 0.020 O1MET add CM HM2 single 0.960 0.020 O1MET add CM HM3 single 0.960 0.020

Example of peptide link

Link formalism allows to join monomers together

Link describes in details the result of chemical reaction

R2H

NH3+

O

OR1H

NH3+

O

N

H O

O

HR2

R1H

NH3+

O

O+

H2O

Link: general categorydata_link_listloop__chem_link.id_chem_link.comp_id_1_chem_link.mod_id_1_chem_link.group_comp_1_chem_link.comp_id_2_chem_link.mod_id_2_chem_link.group_comp_2_chem_link.nameALPHA1-4 . DEL-HO4 pyranose . DEL-O1 pyranose glycosidic_bond_alpha1-4

mod_id _1: modification of first monomer before the linkage mod_id_2 : modification of second monomer before the linkage

Link: bond categoryloop__chem_link_bond.link_id_chem_link_bond.atom_1_comp_id_chem_link_bond.atom_id_1_chem_link_bond.atom_2_comp_id_chem_link_bond.atom_id_2_chem_link_bond.type_chem_link_bond.value_dist_chem_link_bond.value_dist_esd ALPHA1-4 1 O4 2 C1 single 1.439 0.020

atom_1_comp_id: means first monomeratom_2_comp_id: means second monomer

Source of dictionary and coordinates

• MSDchem• PRODRG• RELIBASE• CORINA• QM or other energy minimsation programs• CSD

MSDchemYou can search by formula, substructure and others. Results can be

save as cif file and used by libcheck to create dictionary for refmac

MSDchem: JME

1) Draw substructure,

write a smile file or

load SDF, MOL, mmCIF,

2) Search

PRODRG server

JME

Load your file

PRODRG: JME

Draw your ligand,

transfer to PRODRG

window and run

PRODRG output

It can write out

dictionaries for CNS

REFMAC5, SHELX

and others

Tools in CCP4

LIBCHECK - creates the complete monomer description from minimal - creates coordinates from complete monomer description

SKETCHER - graphical program that creates the minimal monomer description for LIBCHECK

MAKECIF - creates restraints

Ways to create dictionary

1. From chemical structure

2. From Cartesian coordinates

Using SKETCHER: monomer is drawn specifyingatoms and bondsFrom SMILE strings, sdf file, mol2 file

Coordinates from CSDEnergetically optimised coordinatesMOL2 fileSDF file

Smile strings: An example

SMILE for ALA:N[C@@H](C)C(=O)O

3D representation:

For description of smile:

http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html

SketcherInitial 2D sketch

After LIBCHECK and REFMAC

Restraints:monomer linkage

1. Chain links (trans/cis, DNA/RNA, sugar links, gap)

2. Standard links (SS bridges, sugar-protein links)

3. Potential links4. Links between alternative conformations5. Symmetry links6. User links

Modifications and links in PDB file

SSBOND 1 CYS L 88 CYS L 23LINK SG CYS H 195 2.031 SG BCYS H 140 SSLINK TYR L 139 PRO L 140 PCISLINK GLY H 127 GLY H 133 gapLINK MAG Y 1 GAL Y 2 BETA1-4LINK O LEU B 61 NA NA X 6 LEU-NALINK OE1 GLU A 139 NA NA X 1 12555 symmetry

MODRES GAL Y 2 GAL-b-D RENAME

Modification IDStandard nameName in PDB file

Link ID

Conclusions

• Ligand dictionaries should designed with care. Interpetation of chemistry may depend on that

• Such resources as MSDchem, PRODRG can help to create an accurate dictionary

• Links and modifications are important component for understanding protein chemistry

• Unfortunately no automatic link generation programs available yet (we are working on that)

Acknowledgments

• Alexei Vagin – YSBL, York• Roberto Steiner – Kings coll.• Andrey Lebedev – YSBL, York• Liz Potterton – YSBL, York• Fei Long – YSBL, York

• Wellcome Trust, BBSRC, BIOXHIT, CCP4 – money