data_VC9
#
_chem_comp.id VC9
_chem_comp.name "2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H16 Br2 N3 O12 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-03-26
_chem_comp.pdbx_modified_date 2018-06-15
_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 622.976
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VC9
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 6CTX
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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.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
VC9 C4 C1 C 0 1 N N N 9.320 7.594 11.036 -7.456 -2.728 0.435 C4 VC9 1
VC9 N4 N1 N 0 1 N N N 10.781 7.611 11.275 -8.197 -3.747 0.987 N4 VC9 2
VC9 C5 C2 C 0 1 N N N 8.489 7.267 12.066 -7.203 -2.706 -0.952 C5 VC9 3
VC9 C6 C3 C 0 1 N N N 7.115 7.239 11.771 -6.470 -1.692 -1.470 C6 VC9 4
VC9 N3 N2 N 0 1 N N N 8.831 7.880 9.831 -6.978 -1.758 1.204 N3 VC9 5
VC9 C2 C4 C 0 1 N N N 7.534 7.841 9.619 -6.259 -0.767 0.680 C2 VC9 6
VC9 O2 O1 O 0 1 N N N 7.084 8.103 8.480 -5.830 0.113 1.408 O2 VC9 7
VC9 N1 N3 N 0 1 N N N 6.674 7.520 10.574 -5.996 -0.721 -0.639 N1 VC9 8
VC9 "C1'" C5 C 0 1 N N R 5.357 7.475 10.288 -5.201 0.381 -1.186 "C1'" VC9 9
VC9 "C2'" C6 C 0 1 N N N 4.922 6.031 9.800 -5.918 1.729 -0.950 "C2'" VC9 10
VC9 "C3'" C7 C 0 1 N N S 4.498 5.466 10.905 -4.769 2.716 -0.641 "C3'" VC9 11
VC9 "O3'" O2 O 0 1 N N N 3.589 4.299 10.743 -4.730 3.760 -1.615 "O3'" VC9 12
VC9 "O4'" O3 O 0 1 N N N 4.455 7.692 11.520 -3.949 0.499 -0.476 "O4'" VC9 13
VC9 "C4'" C8 C 0 1 N N R 3.683 6.661 11.656 -3.495 1.847 -0.727 "C4'" VC9 14
VC9 "C5'" C9 C 0 1 N N N 3.466 6.294 13.155 -2.484 2.275 0.339 "C5'" VC9 15
VC9 "O5'" O4 O 0 1 N N N 4.677 6.233 13.817 -1.271 1.541 0.167 "O5'" VC9 16
VC9 PA P1 P 0 1 N N N 5.010 4.986 14.840 0.014 1.736 1.117 PA VC9 17
VC9 O1A O5 O 0 1 N N N 3.993 4.909 15.897 -0.348 1.267 2.614 O1A VC9 18
VC9 O2A O6 O 0 1 N N N 6.391 5.111 15.392 0.406 3.163 1.129 O2A VC9 19
VC9 O3A O7 O 0 1 N N N 5.023 3.668 13.950 1.236 0.849 0.558 O3A VC9 20
VC9 PB P2 P 0 1 N N N 3.896 2.403 13.966 2.821 0.826 0.837 PB VC9 21
VC9 O1B O8 O 0 1 N N N 2.553 2.838 14.463 3.455 2.255 0.453 O1B VC9 22
VC9 O2B O9 O 0 1 N N N 3.783 1.945 12.486 3.065 0.547 2.270 O2B VC9 23
VC9 C3B C10 C 0 1 N N N 4.643 1.109 15.022 3.597 -0.476 -0.176 C3B VC9 24
VC9 BR1 BR1 BR 0 0 N N N 6.519 1.378 15.335 2.823 -2.221 0.293 BR1 VC9 25
VC9 BR2 BR2 BR 0 0 N N N 4.707 -0.643 14.210 3.273 -0.105 -2.080 BR2 VC9 26
VC9 PG P3 P 0 1 N N N 3.826 0.993 16.680 5.392 -0.503 0.140 PG VC9 27
VC9 O2G O10 O 0 1 N N N 3.732 2.421 17.230 5.658 -0.806 1.699 O2G VC9 28
VC9 O1G O11 O 0 1 N N N 4.758 0.186 17.594 6.078 -1.652 -0.755 O1G VC9 29
VC9 O3G O12 O 0 1 N N N 2.537 0.292 16.580 5.975 0.811 -0.213 O3G VC9 30
VC9 H1 H1 H 0 1 N N N 11.407 7.838 10.529 -8.549 -4.452 0.422 H1 VC9 31
VC9 H2 H2 H 0 1 N N N 11.142 7.395 12.182 -8.369 -3.759 1.942 H2 VC9 32
VC9 H3 H3 H 0 1 N N N 8.865 7.042 13.053 -7.589 -3.486 -1.592 H3 VC9 33
VC9 H4 H4 H 0 1 N N N 6.411 6.980 12.548 -6.264 -1.653 -2.529 H4 VC9 34
VC9 H5 H5 H 0 1 N N N 5.082 8.203 9.510 -5.021 0.227 -2.250 H5 VC9 35
VC9 H6 H6 H 0 1 N N N 4.118 6.091 9.052 -6.456 2.038 -1.845 H6 VC9 36
VC9 H7 H7 H 0 1 N N N 5.776 5.482 9.377 -6.597 1.657 -0.101 H7 VC9 37
VC9 H8 H8 H 0 1 N N N 5.334 5.179 11.560 -4.881 3.131 0.361 H8 VC9 38
VC9 H9 H9 H 0 1 N N N 3.801 3.639 11.393 -5.532 4.300 -1.646 H9 VC9 39
VC9 H10 H10 H 0 1 N N N 2.706 6.778 11.165 -3.053 1.919 -1.721 H10 VC9 40
VC9 H11 H11 H 0 1 N N N 2.833 7.060 13.627 -2.281 3.342 0.238 H11 VC9 41
VC9 H12 H12 H 0 1 N N N 2.968 5.315 13.220 -2.894 2.075 1.329 H12 VC9 42
VC9 H13 H13 H 0 1 N N N 4.415 4.954 16.747 -0.615 0.340 2.682 H13 VC9 43
VC9 H14 H14 H 0 1 N N N 1.912 2.743 13.769 3.332 2.503 -0.474 H14 VC9 44
VC9 H15 H15 H 0 1 N N N 2.825 2.627 17.423 5.303 -1.653 2.001 H15 VC9 45
VC9 H16 H16 H 0 1 N N N 4.307 -0.592 17.900 7.035 -1.723 -0.637 H16 VC9 46
#
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
VC9 O2 C2 DOUB N N 1
VC9 C2 N3 SING N N 2
VC9 C2 N1 SING N N 3
VC9 "C2'" "C1'" SING N N 4
VC9 "C2'" "C3'" SING N N 5
VC9 N3 C4 DOUB N N 6
VC9 "C1'" N1 SING N N 7
VC9 "C1'" "O4'" SING N N 8
VC9 N1 C6 SING N N 9
VC9 "O3'" "C3'" SING N N 10
VC9 "C3'" "C4'" SING N N 11
VC9 C4 N4 SING N N 12
VC9 C4 C5 SING N N 13
VC9 "O4'" "C4'" SING N N 14
VC9 "C4'" "C5'" SING N N 15
VC9 C6 C5 DOUB N N 16
VC9 O2B PB DOUB N N 17
VC9 "C5'" "O5'" SING N N 18
VC9 "O5'" PA SING N N 19
VC9 O3A PB SING N N 20
VC9 O3A PA SING N N 21
VC9 PB O1B SING N N 22
VC9 PB C3B SING N N 23
VC9 BR2 C3B SING N N 24
VC9 PA O2A DOUB N N 25
VC9 PA O1A SING N N 26
VC9 C3B BR1 SING N N 27
VC9 C3B PG SING N N 28
VC9 O3G PG DOUB N N 29
VC9 PG O2G SING N N 30
VC9 PG O1G SING N N 31
VC9 N4 H1 SING N N 32
VC9 N4 H2 SING N N 33
VC9 C5 H3 SING N N 34
VC9 C6 H4 SING N N 35
VC9 "C1'" H5 SING N N 36
VC9 "C2'" H6 SING N N 37
VC9 "C2'" H7 SING N N 38
VC9 "C3'" H8 SING N N 39
VC9 "O3'" H9 SING N N 40
VC9 "C4'" H10 SING N N 41
VC9 "C5'" H11 SING N N 42
VC9 "C5'" H12 SING N N 43
VC9 O1A H13 SING N N 44
VC9 O1B H14 SING N N 45
VC9 O2G H15 SING N N 46
VC9 O1G H16 SING N N 47
#
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
VC9 SMILES ACDLabs 12.01 "C=1(N)C=CN(C(N=1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(Br)(P(O)(O)=O)Br)=O"
VC9 InChI InChI 1.03 "InChI=1S/C10H16Br2N3O12P3/c11-10(12,28(18,19)20)29(21,22)27-30(23,24)25-4-6-5(16)3-8(26-6)15-2-1-7(13)14-9(15)17/h1-2,5-6,8,16H,3-4H2,(H,21,22)(H,23,24)(H2,13,14,17)(H2,18,19,20)/t5-,6+,8+/m0/s1"
VC9 InChIKey InChI 1.03 QBTCYYWCAIICFQ-SHYZEUOFSA-N
VC9 SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)C(Br)(Br)[P](O)(O)=O)O2"
VC9 SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(Br)(Br)[P](O)(O)=O)O2"
VC9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Br)Br)O)O"
VC9 SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Br)Br)O)O"
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
VC9 "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine"
VC9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-bis(bromanyl)methyl]phosphonic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VC9 "Create component" 2018-03-26 RCSB
VC9 "Initial release" 2018-06-20 RCSB
#