data_MSS
#
_chem_comp.id MSS
_chem_comp.name (MOLYBDOPTERIN-S,S)-OXO-MOLYBDENUM
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H12 Mo N5 O7 P S2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-03-04
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 505.275
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code MSS
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag Y
_chem_comp.pdbx_model_coordinates_db_code 2BLF
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
MSS N1 N1 N 0 1 Y N N N N N 69.624 13.175 21.096 ? ? ? N1 MSS 1
MSS C2 C2 C 0 1 Y N N N N N 70.357 14.300 20.963 ? ? ? C2 MSS 2
MSS N2 N2 N 0 1 N N N N N N 70.083 15.150 19.959 ? ? ? N2 MSS 3
MSS N3 N3 N 0 1 Y N N N N N 71.391 14.608 21.787 ? ? ? N3 MSS 4
MSS C4 C4 C 0 1 Y N N N N N 71.740 13.808 22.830 ? ? ? C4 MSS 5
MSS O4 O4 O 0 1 N N N N N N 72.694 14.108 23.580 ? ? ? O4 MSS 6
MSS N5 N5 N 0 1 N N N N N N 71.273 11.668 24.020 ? ? ? N5 MSS 7
MSS C6 C6 C 0 1 N N R N N N 70.797 10.302 23.869 ? ? ? C6 MSS 8
MSS C7 C7 C 0 1 N N R N N N 69.394 10.238 23.264 ? ? ? C7 MSS 9
MSS N8 N8 N 0 1 N N N N N N 69.167 11.212 22.234 ? ? ? N8 MSS 10
MSS C9 C9 C 0 1 Y N N N N N 70.973 12.581 23.061 ? ? ? C9 MSS 11
MSS C10 C10 C 0 1 Y N N N N N 69.885 12.318 22.112 ? ? ? C10 MSS 12
MSS "C1'" "C1'" C 0 1 N N N N N N 70.914 9.401 25.071 ? ? ? "C1'" MSS 13
MSS "S1'" "S1'" S 0 1 N N N N N N 72.483 8.892 25.511 ? ? ? "S1'" MSS 14
MSS "C2'" "C2'" C 0 1 N N N N N N 69.805 8.934 25.676 ? ? ? "C2'" MSS 15
MSS "S2'" "S2'" S 0 1 N N N N N N 69.922 7.752 26.900 ? ? ? "S2'" MSS 16
MSS "C3'" "C3'" C 0 1 N N R N N N 68.421 9.394 25.253 ? ? ? "C3'" MSS 17
MSS "O3'" "O3'" O 0 1 N N N N N N 68.410 10.439 24.259 ? ? ? "O3'" MSS 18
MSS "C4'" "C4'" C 0 1 N N N N N N 67.621 9.892 26.435 ? ? ? "C4'" MSS 19
MSS "O4'" "O4'" O 0 1 N N N N N N 66.338 10.349 25.969 ? ? ? "O4'" MSS 20
MSS P P P 0 1 N N N N N N 65.442 11.276 26.940 ? ? ? P MSS 21
MSS O1P O1P O 0 1 N N N N N N 66.326 12.426 27.334 ? ? ? O1P MSS 22
MSS O2P O2P O 0 1 N N N N N N 65.104 10.322 28.096 ? ? ? O2P MSS 23
MSS O3P O3P O 0 1 N N N N N N 64.205 11.587 26.179 ? ? ? O3P MSS 24
MSS MOM1 MOM1 MO 0 0 N N N N N N 72.282 7.090 27.084 ? ? ? MOM1 MSS 25
MSS OM1 OM1 O 0 1 N N N N N N 72.591 5.619 26.201 ? ? ? OM1 MSS 26
MSS H2N1 1H2N H 0 0 N N N N N N 70.637 16.000 19.858 ? ? ? H2N1 MSS 27
MSS H2N2 2H2N H 0 0 N N N N N N 69.306 14.919 19.340 ? ? ? H2N2 MSS 28
MSS H3 H3 H 0 1 N N N N N N 71.921 15.463 21.619 ? ? ? H3 MSS 29
MSS H5 H5 H 0 1 N N N N N N 71.825 11.936 24.835 ? ? ? H5 MSS 30
MSS H6 H6 H 0 1 N N N N N N 71.464 9.847 23.100 ? ? ? H6 MSS 31
MSS H7 H7 H 0 1 N N N N N N 69.247 9.223 22.826 ? ? ? H7 MSS 32
MSS H8 H8 H 0 1 N N N N N N 68.417 11.044 21.564 ? ? ? H8 MSS 33
MSS "H3'" "H3'" H 0 1 N N N N N N 67.886 8.514 24.827 ? ? ? "H3'" MSS 34
MSS "H4'1" "1H4'" H 0 0 N N N N N N 68.164 10.672 27.018 ? ? ? "H4'1" MSS 35
MSS "H4'2" "2H4'" H 0 0 N N N N N N 67.533 9.127 27.242 ? ? ? "H4'2" MSS 36
MSS HP1 1HP H 0 1 N N N N N N 65.798 12.971 27.905 ? ? ? HP1 MSS 37
MSS HP2 2HP H 0 1 N N N N N N 64.576 10.867 28.667 ? ? ? HP2 MSS 38
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
MSS N1 C2 DOUB Y N 1
MSS N1 C10 SING Y N 2
MSS C2 N2 SING N N 3
MSS C2 N3 SING Y N 4
MSS N2 H2N1 SING N N 5
MSS N2 H2N2 SING N N 6
MSS N3 C4 SING Y N 7
MSS N3 H3 SING N N 8
MSS C4 O4 DOUB N N 9
MSS C4 C9 SING Y N 10
MSS N5 C6 SING N N 11
MSS N5 C9 SING N N 12
MSS N5 H5 SING N N 13
MSS C6 C7 SING N N 14
MSS C6 "C1'" SING N N 15
MSS C6 H6 SING N N 16
MSS C7 N8 SING N N 17
MSS C7 "O3'" SING N N 18
MSS C7 H7 SING N N 19
MSS N8 C10 SING N N 20
MSS N8 H8 SING N N 21
MSS C9 C10 DOUB Y N 22
MSS "C1'" "S1'" SING N N 23
MSS "C1'" "C2'" DOUB N N 24
MSS "S1'" MOM1 SING N N 25
MSS "C2'" "S2'" SING N N 26
MSS "C2'" "C3'" SING N N 27
MSS "S2'" MOM1 SING N N 28
MSS "C3'" "O3'" SING N N 29
MSS "C3'" "C4'" SING N N 30
MSS "C3'" "H3'" SING N N 31
MSS "C4'" "O4'" SING N N 32
MSS "C4'" "H4'1" SING N N 33
MSS "C4'" "H4'2" SING N N 34
MSS "O4'" P SING N N 35
MSS P O1P SING N N 36
MSS P O2P SING N N 37
MSS P O3P DOUB N N 38
MSS O1P HP1 SING N N 39
MSS O2P HP2 SING N N 40
MSS MOM1 OM1 DOUB N N 41
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
MSS SMILES ACDLabs 10.04 O=P(O)(O)OCC2OC3NC=4N=C(N)NC(=O)C=4NC3C=1S[Mo](=O)SC=12
MSS SMILES_CANONICAL CACTVS 3.341 NC1=NC2=C(N[C@@H]3[C@H](N2)O[C@H](CO[P](O)(O)=O)C4=C3S[Mo](=O)S4)C(=O)N1
MSS SMILES CACTVS 3.341 NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(O)=O)C4=C3S[Mo](=O)S4)C(=O)N1
MSS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H]1C2=C([C@H]3[C@@H](O1)NC4=C(N3)C(=O)NC(=N4)N)S[Mo](=O)S2)OP(=O)(O)O
MSS SMILES "OpenEye OEToolkits" 1.5.0 C(C1C2=C(C3C(O1)NC4=C(N3)C(=O)NC(=N4)N)S[Mo](=O)S2)OP(=O)(O)O
MSS InChI InChI 1.03 InChI=1S/C10H14N5O6PS2.Mo.O/c11-10-14-7-4(8(16)15-10)12-3-6(24)5(23)2(21-9(3)13-7)1-20-22(17,18)19;;/h2-3,9,12,23-24H,1H2,(H2,17,18,19)(H4,11,13,14,15,16);;/q;+2;/p-2/t2-,3+,9-;;/m1../s1
MSS InChIKey InChI 1.03 BDXDYZBRBRKVRM-MRZGRPIRSA-L
#
_pdbx_chem_comp_identifier.comp_id MSS
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program ACDLabs
_pdbx_chem_comp_identifier.program_version 10.04
_pdbx_chem_comp_identifier.identifier oxo(phosphate)molybdenum
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
MSS 'Create component' 2005-03-04 EBI
MSS 'Modify descriptor' 2011-06-04 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
MSS N1 N 4.666 -1.687 1
MSS C2 C 5.969 -0.940 2
MSS N2 N 7.266 -1.691 3
MSS N3 N 5.968 0.560 4
MSS C4 C 4.672 1.313 5
MSS O4 O 4.672 2.812 6
MSS N5 N 2.073 1.316 7
MSS C6 C 0.771 0.564 8
MSS C7 C 0.772 -0.935 9
MSS N8 N 2.069 -1.684 10
MSS C9 C 3.370 0.563 11
MSS C10 C 3.370 -0.936 12
MSS "C1'" C -0.527 1.318 13
MSS "S1'" S -0.837 2.784 14
MSS "C2'" C -1.825 0.568 15
MSS "S2'" S -2.939 1.574 16
MSS "C3'" C -1.828 -0.932 17
MSS "O3'" O -0.529 -1.681 18
MSS "C4'" C -3.126 -1.680 19
MSS "O4'" O -4.425 -0.929 20
MSS P P -5.724 -1.679 21
MSS O1P O -6.473 -0.379 22
MSS O2P O -4.975 -2.978 23
MSS O3P O -7.024 -2.428 24
MSS MOM1 Mo -2.329 2.944 25
MSS OM1 O -3.077 4.243 26
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
MSS N1 C2 DOUBLE NONE 1
MSS N1 C10 SINGLE NONE 2
MSS C2 N2 SINGLE NONE 3
MSS C2 N3 SINGLE NONE 4
MSS N3 C4 SINGLE NONE 5
MSS C4 O4 DOUBLE NONE 6
MSS C4 C9 SINGLE NONE 7
MSS N5 C6 SINGLE NONE 8
MSS N5 C9 SINGLE NONE 9
MSS C6 C7 SINGLE NONE 10
MSS C6 "C1'" SINGLE NONE 11
MSS C7 N8 SINGLE NONE 12
MSS C7 "O3'" SINGLE NONE 13
MSS N8 C10 SINGLE NONE 14
MSS C9 C10 DOUBLE NONE 15
MSS "C1'" "S1'" SINGLE NONE 16
MSS "C1'" "C2'" DOUBLE NONE 17
MSS "S1'" MOM1 SINGLE NONE 18
MSS "C2'" "S2'" SINGLE NONE 19
MSS "C2'" "C3'" SINGLE NONE 20
MSS "S2'" MOM1 SINGLE NONE 21
MSS "C3'" "O3'" SINGLE NONE 22
MSS "C3'" "C4'" SINGLE BEGINDASH 23
MSS "C4'" "O4'" SINGLE NONE 24
MSS "O4'" P SINGLE NONE 25
MSS P O1P SINGLE NONE 26
MSS P O2P SINGLE NONE 27
MSS P O3P DOUBLE NONE 28
MSS MOM1 OM1 DOUBLE NONE 29
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
MSS MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1N[C@H]1C3=C(CO[C@H]1N2)S[Mo](=O)S3' 'InChI=1S/C9H10N4O2S2.Mo.O/c14-8-5-7(10-2-11-8)13-9-4(12-5)6(17)3(16)1-15-9;;/h2,4,9,12,16-17H,1H2,(H2,10,11,13,14);;/q;+2;/p-2/t4-,9+;;/m0../s1' PMYAFUIFWZDAAP-FWRUFDEASA-L
MSS phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
MSS pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
MSS N1 S1 1
MSS C2 S1 1
MSS N3 S1 1
MSS C4 S1 1
MSS O4 S1 1
MSS N5 S1 1
MSS C6 S1 1
MSS C7 S1 1
MSS N8 S1 1
MSS C9 S1 1
MSS C10 S1 1
MSS "C1'" S1 1
MSS "S1'" S1 1
MSS "C2'" S1 1
MSS "S2'" S1 1
MSS "C3'" S1 1
MSS "O3'" S1 1
MSS MOM1 S1 1
MSS OM1 S1 1
MSS "O4'" F1 1
MSS P F1 1
MSS O3P F1 1
MSS O1P F1 1
MSS O2P F1 1
MSS C9 F2 1
MSS C4 F2 1
MSS N3 F2 1
MSS C2 F2 1
MSS N1 F2 1
MSS C10 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id MSS
_pdbe_chem_comp_rdkit_properties.exactmw 506.897
_pdbe_chem_comp_rdkit_properties.amw 505.282
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 12
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 7
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 13
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 26
_pdbe_chem_comp_rdkit_properties.NumAtoms 38
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 16
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.400
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 174.078
_pdbe_chem_comp_rdkit_properties.tpsa 188.890
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.364
_pdbe_chem_comp_rdkit_properties.CrippenMR 87.491
_pdbe_chem_comp_rdkit_properties.chi0v 16.300
_pdbe_chem_comp_rdkit_properties.chi1v 14.897
_pdbe_chem_comp_rdkit_properties.chi2v 11.551
_pdbe_chem_comp_rdkit_properties.chi3v 11.551
_pdbe_chem_comp_rdkit_properties.chi4v 11.894
_pdbe_chem_comp_rdkit_properties.chi0n 23.766
_pdbe_chem_comp_rdkit_properties.chi1n 11.770
_pdbe_chem_comp_rdkit_properties.chi2n 2.835
_pdbe_chem_comp_rdkit_properties.chi3n 2.835
_pdbe_chem_comp_rdkit_properties.chi4n 1.940
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.722
_pdbe_chem_comp_rdkit_properties.kappa1 9.184
_pdbe_chem_comp_rdkit_properties.kappa2 6.710
_pdbe_chem_comp_rdkit_properties.kappa3 3.522
_pdbe_chem_comp_rdkit_properties.Phi 2.370
#
_pdbe_chem_comp_external_mappings.comp_id MSS
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id MSS
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
MSS N1 3.401 1.545 1.297 ETKDGv3 1
MSS C2 4.633 1.227 1.574 ETKDGv3 2
MSS N2 5.415 2.078 2.411 ETKDGv3 3
MSS N3 5.202 0.025 1.037 ETKDGv3 4
MSS C4 4.396 -0.815 0.208 ETKDGv3 5
MSS O4 4.871 -1.879 -0.270 ETKDGv3 6
MSS N5 2.146 -1.220 -0.879 ETKDGv3 7
MSS C6 0.703 -0.981 -0.960 ETKDGv3 8
MSS C7 0.365 0.537 -0.820 ETKDGv3 9
MSS N8 1.213 1.164 0.197 ETKDGv3 10
MSS C9 3.006 -0.411 -0.067 ETKDGv3 11
MSS C10 2.554 0.736 0.460 ETKDGv3 12
MSS "C1'" -0.056 -1.765 0.083 ETKDGv3 13
MSS "S1'" 0.691 -3.240 0.828 ETKDGv3 14
MSS "C2'" -1.355 -1.430 0.267 ETKDGv3 15
MSS "S2'" -2.465 -2.409 1.318 ETKDGv3 16
MSS "C3'" -1.880 -0.276 -0.582 ETKDGv3 17
MSS "O3'" -0.998 0.833 -0.498 ETKDGv3 18
MSS "C4'" -3.282 0.185 -0.167 ETKDGv3 19
MSS "O4'" -3.669 1.270 -0.976 ETKDGv3 20
MSS P -5.192 1.823 -0.443 ETKDGv3 21
MSS O1P -5.080 2.372 1.156 ETKDGv3 22
MSS O2P -6.337 0.580 -0.546 ETKDGv3 23
MSS O3P -5.631 2.968 -1.327 ETKDGv3 24
MSS MOM1 -1.403 -4.451 0.506 ETKDGv3 25
MSS OM1 -1.728 -4.632 -1.272 ETKDGv3 26
MSS H2N1 5.008 2.955 2.804 ETKDGv3 27
MSS H2N2 6.404 1.832 2.638 ETKDGv3 28
MSS H3 6.190 -0.237 1.251 ETKDGv3 29
MSS H5 2.531 -2.074 -1.342 ETKDGv3 30
MSS H6 0.355 -1.324 -1.960 ETKDGv3 31
MSS H7 0.595 1.022 -1.793 ETKDGv3 32
MSS H8 0.883 2.047 0.647 ETKDGv3 33
MSS "H3'" -1.946 -0.612 -1.642 ETKDGv3 34
MSS "H4'1" -3.989 -0.663 -0.308 ETKDGv3 35
MSS "H4'2" -3.250 0.482 0.907 ETKDGv3 36
MSS HP1 -6.006 2.620 1.404 ETKDGv3 37
MSS HP2 -6.294 0.118 0.329 ETKDGv3 38
#