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DR9 : Summary

Code

DR9

One-letter code

X

Molecule name

1-CIS-9-OCTADECANOYL-2-CIS-9-HEXADECANOYL PHOSPHATIDYL GLYCEROL

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R)-3-{[(S)-{[(2R)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(9Z)-hexadec-9-enoyloxy]propyl (9Z)-octadec-9-enoate
OpenEye OEToolkits 1.5.0 [(2R)-3-[[(2R)-2,3-dihydroxypropoxy]-hydroxy-phosphoryl]oxy-2-[(Z)-hexadec-9-enoyl]oxy-propyl] (Z)-octadec-9-enoate

Formula

C40 H75 O10 P

Formal charge

0

Molecular weight

746.991 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(OC(COP(=O)(OCC(O)CO)O)COC(=O)CCCCCCC\C=C/CCCCCCCC)CCCCCCC\C=C/CCCCCC
SMILES CACTVS 3.341 CCCCCCCCC=CCCCCCCCC(=O)OC[CH](CO[P](O)(=O)OC[CH](O)CO)OC(=O)CCCCCCCC=CCCCCCC
SMILES OpenEye OEToolkits 1.5.0 CCCCCCCCC=CCCCCCCCC(=O)OCC(COP(=O)(O)OCC(CO)O)OC(=O)CCCCCCCC=CCCCCCC
Canonical SMILES CACTVS 3.341 CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@H](CO[P@](O)(=O)OC[C@H](O)CO)OC(=O)CCCCCCC\C=C/CCCCCC
Canonical SMILES OpenEye OEToolkits 1.5.0 CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@@H](CO)O)OC(=O)CCCCCCC\C=C/CCCCCC

IUPAC InChI

InChI=1S/C40H75O10P/c1-3-5-7-9-11-13-15-17-18-20-21-23-25-27-29-31-39(43)47-35-38(36-49-51(45,46)48-34-37(42)33-41)50-40(44)32-30-28-26-24-22-19-16-14-12-10-8-6-4-2/h14,16-18,37-38,41-42H,3-13,15,19-36H2,1-2H3,(H,45,46)/b16-14-,18-17-/t37-,38-/m1/s1

IUPAC InChI key

QGIXWNRQEFVVRM-CTDKCSBDSA-N
DR9

wwPDB Information

Atom count

126 (51 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-02-25

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



DR9 : Atoms of Molecule

Total Number of Atoms: 126
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CBX C CBX N N N 0 -16.498 4.291 5.015
2 CBV C CBV N N N 0 -15.437 3.441 4.313
3 CBS C CBS N N N 0 -15.071 4.086 2.975
4 CBH C CBH N N N 0 -14.01 3.237 2.272
5 CAQ C CAQ N N N 0 -13.645 3.882 0.934
6 CAP C CAP N N N 0 -12.584 3.033 0.231
7 CAO C CAO N N N 0 -12.218 3.678 -1.107
8 CAN C CAN N N N 0 -11.157 2.828 -1.81
9 CAM C CAM N N N 0 -10.797 3.464 -3.128
10 CAL C CAL N N N 0 -9.542 3.702 -3.419
11 CAK C CAK N N N 0 -8.449 3.191 -2.517
12 CAJ C CAJ N N N 0 -7.446 2.38 -3.34
13 CAI C CAI N N N 0 -6.336 1.86 -2.424
14 CAH C CAH N N N 0 -5.334 1.049 -3.247
15 CAG C CAG N N N 0 -4.224 0.53 -2.331
16 CAF C CAF N N N 0 -3.221 -0.282 -3.154
17 CAE C CAE N N N 0 -2.111 -0.801 -2.238
18 CAD C CAD N N N 0 -1.124 -1.6 -3.048
19 OAA O OAA N N N 0 -1.291 -1.74 -4.237
20 OAC O OAC N N N 0 -0.059 -2.156 -2.45
21 CAB C CAB N N N 0 0.893 -2.926 -3.231
22 CBE C CBE R N N 0 2.003 -3.446 -2.315
23 CBK C CBK N N N 0 1.383 -4.233 -1.159
24 OBL O OBL N N N 0 0.424 -3.416 -0.485
25 PBM P PBM S N N 0 -0.184 -4.303 0.713
26 OBU O OBU N N N 0 -0.719 -5.569 0.165
27 OBF O OBF N N N 0 0.975 -4.627 1.782
28 OBN O OBN N N N 0 -1.369 -3.487 1.436
29 CBO C CBO N N N 0 -1.944 -4.367 2.405
30 CBP C CBP R N N 0 -3.083 -3.649 3.132
31 OBG O OBG N N N 0 -2.554 -2.554 3.882
32 CBQ C CBQ N N N 0 -3.778 -4.628 4.08
33 OBR O OBR N N N 0 -4.913 -3.992 4.673
34 OBD O OBD N N N 0 2.758 -2.324 -1.786
35 CBC C CBC N N N 0 4.058 -2.472 -1.487
36 OBJ O OBJ N N N 0 4.6 -3.539 -1.657
37 CBB C CBB N N N 0 4.843 -1.308 -0.938
38 CBA C CBA N N N 0 6.288 -1.741 -0.684
39 CAZ C CAZ N N N 0 7.084 -0.559 -0.127
40 CAY C CAY N N N 0 8.529 -0.992 0.128
41 CAX C CAX N N N 0 9.325 0.19 0.685
42 CAW C CAW N N N 0 10.77 -0.243 0.939
43 CAV C CAV N N N 0 11.566 0.939 1.496
44 CAU C CAU N N N 0 12.99 0.512 1.747
45 CAT C CAT N N N 0 13.98 1.209 1.246
46 CAS C CAS N N N 0 13.707 2.525 0.567
47 CAR C CAR N N N 0 14.576 3.615 1.198
48 CBI C CBI N N N 0 14.299 4.952 0.508
49 CBT C CBT N N N 0 15.168 6.042 1.139
50 CBW C CBW N N N 0 14.891 7.379 0.449
51 CBY C CBY N N N 0 15.76 8.468 1.08
52 HBX1 H 1HBX N N N 0 -16.104 5.292 5.19
53 HBX2 H 2HBX N N N 0 -17.387 4.354 4.388
54 HBX3 H 3HBX N N N 0 -16.758 3.831 5.969
55 HBV1 H 1HBV N N N 0 -14.548 3.378 4.941
56 HBV2 H 2HBV N N N 0 -15.83 2.44 4.138
57 HBS1 H 1HBS N N N 0 -15.96 4.15 2.347
58 HBS2 H 2HBS N N N 0 -14.678 5.088 3.149
59 HBH1 H 1HBH N N N 0 -13.121 3.174 2.9
60 HBH2 H 2HBH N N N 0 -14.403 2.236 2.097
61 HAQ1 H 1HAQ N N N 0 -14.534 3.945 0.306
62 HAQ2 H 2HAQ N N N 0 -13.251 4.883 1.108
63 HAP1 H 1HAP N N N 0 -11.695 2.97 0.859
64 HAP2 H 2HAP N N N 0 -12.977 2.031 0.056
65 HAO1 H 1HAO N N N 0 -13.107 3.741 -1.735
66 HAO2 H 2HAO N N N 0 -11.825 4.679 -0.933
67 HAN1 H 1HAN N N N 0 -10.268 2.765 -1.182
68 HAN2 H 2HAN N N N 0 -11.55 1.827 -1.985
69 HAM H HAM N N N 0 -11.574 3.722 -3.833
70 HAL H HAL N N N 0 -9.292 4.266 -4.306
71 HAK1 H 1HAK N N N 0 -7.939 4.034 -2.051
72 HAK2 H 2HAK N N N 0 -8.883 2.556 -1.744
73 HAJ1 H 1HAJ N N N 0 -7.957 1.537 -3.806
74 HAJ2 H 2HAJ N N N 0 -7.013 3.014 -4.113
75 HAI1 H 1HAI N N N 0 -5.826 2.703 -1.958
76 HAI2 H 2HAI N N N 0 -6.77 1.226 -1.651
77 HAH1 H 1HAH N N N 0 -5.844 0.206 -3.713
78 HAH2 H 2HAH N N N 0 -4.9 1.684 -4.02
79 HAG1 H 1HAG N N N 0 -3.713 1.373 -1.865
80 HAG2 H 2HAG N N N 0 -4.658 -0.105 -1.558
81 HAF1 H 1HAF N N N 0 -3.731 -1.124 -3.62
82 HAF2 H 2HAF N N N 0 -2.787 0.353 -3.927
83 HAE1 H 1HAE N N N 0 -1.601 0.042 -1.772
84 HAE2 H 2HAE N N N 0 -2.545 -1.435 -1.465
85 HAB1 H 1HAB N N N 0 0.383 -3.769 -3.697
86 HAB2 H 2HAB N N N 0 1.327 -2.292 -4.004
87 HBE H HBE N N N 0 2.668 -4.096 -2.883
88 HBK1 H 1HBK N N N 0 0.891 -5.124 -1.549
89 HBK2 H 2HBK N N N 0 2.166 -4.527 -0.459
90 HBF H HBF N N N 0 1.295 -3.777 2.113
91 HBO1 H 1HBO N N N 0 -2.333 -5.253 1.905
92 HBO2 H 2HBO N N N 0 -1.181 -4.661 3.126
93 HBP H HBP N N N 0 -3.802 -3.276 2.403
94 HBG H HBG N N N 0 -1.924 -2.926 4.514
95 HBQ1 H 1HBQ N N N 0 -4.104 -5.505 3.522
96 HBQ2 H 2HBQ N N N 0 -3.083 -4.932 4.863
97 HBR H HBR N N N 0 -5.322 -4.641 5.261
98 HBB1 H 1HBB N N N 0 4.83 -0.49 -1.658
99 HBB2 H 2HBB N N N 0 4.393 -0.975 -0.002
100 HBA1 H 1HBA N N N 0 6.3 -2.559 0.036
101 HBA2 H 2HBA N N N 0 6.737 -2.073 -1.619
102 HAZ1 H 1HAZ N N N 0 7.071 0.259 -0.847
103 HAZ2 H 2HAZ N N N 0 6.634 -0.227 0.809
104 HAY1 H 1HAY N N N 0 8.542 -1.81 0.848
105 HAY2 H 2HAY N N N 0 8.979 -1.325 -0.808
106 HAX1 H 1HAX N N N 0 9.312 1.008 -0.035
107 HAX2 H 2HAX N N N 0 8.875 0.522 1.62
108 HAW1 H 1HAW N N N 0 10.783 -1.062 1.659
109 HAW2 H 2HAW N N N 0 11.22 -0.576 0.003
110 HAV1 H 1HAV N N N 0 11.554 1.757 0.776
111 HAV2 H 2HAV N N N 0 11.117 1.271 2.432
112 HAU H HAU N N N 0 13.194 -0.368 2.339
113 HAT H HAT N N N 0 14.992 0.839 1.321
114 HAS1 H 1HAS N N N 0 13.942 2.442 -0.495
115 HAS2 H 2HAS N N N 0 12.655 2.785 0.686
116 HAR1 H 1HAR N N N 0 14.341 3.698 2.259
117 HAR2 H 2HAR N N N 0 15.628 3.356 1.078
118 HBI1 H 1HBI N N N 0 14.534 4.869 -0.553
119 HBI2 H 2HBI N N N 0 13.247 5.212 0.627
120 HBT1 H 1HBT N N N 0 14.932 6.125 2.2
121 HBT2 H 2HBT N N N 0 16.22 5.782 1.019
122 HBW1 H 1HBW N N N 0 15.126 7.296 -0.612
123 HBW2 H 2HBW N N N 0 13.839 7.638 0.568
124 HBY1 H 1HBY N N N 0 15.524 8.552 2.141
125 HBY2 H 2HBY N N N 0 16.811 8.209 0.96
126 HBY3 H 3HBY N N N 0 15.562 9.421 0.588



DR9 : Chemical Bonds

Total Number of Bonds: 125
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CBX CBV C C sing 1.53 N N
2 CBX HBX1 C H sing 1.09 N N
3 CBX HBX2 C H sing 1.09 N N
4 CBX HBX3 C H sing 1.09 N N
5 CBV CBS C C sing 1.53 N N
6 CBV HBV1 C H sing 1.09 N N
7 CBV HBV2 C H sing 1.09 N N
8 CBS CBH C C sing 1.53 N N
9 CBS HBS1 C H sing 1.09 N N
10 CBS HBS2 C H sing 1.09 N N
11 CBH CAQ C C sing 1.53 N N
12 CBH HBH1 C H sing 1.09 N N
13 CBH HBH2 C H sing 1.09 N N
14 CAQ CAP C C sing 1.53 N N
15 CAQ HAQ1 C H sing 1.09 N N
16 CAQ HAQ2 C H sing 1.09 N N
17 CAP CAO C C sing 1.53 N N
18 CAP HAP1 C H sing 1.09 N N
19 CAP HAP2 C H sing 1.09 N N
20 CAO CAN C C sing 1.53 N N
21 CAO HAO1 C H sing 1.09 N N
22 CAO HAO2 C H sing 1.09 N N
23 CAN CAM C C sing 1.51 N N
24 CAN HAN1 C H sing 1.09 N N
25 CAN HAN2 C H sing 1.09 N N
26 CAM CAL C C doub 1.31 Z N
27 CAM HAM C H sing 1.08 N N
28 CAL CAK C C sing 1.51 N N
29 CAL HAL C H sing 1.08 N N
30 CAK CAJ C C sing 1.53 N N
31 CAK HAK1 C H sing 1.09 N N
32 CAK HAK2 C H sing 1.09 N N
33 CAJ CAI C C sing 1.53 N N
34 CAJ HAJ1 C H sing 1.09 N N
35 CAJ HAJ2 C H sing 1.09 N N
36 CAI CAH C C sing 1.53 N N
37 CAI HAI1 C H sing 1.09 N N
38 CAI HAI2 C H sing 1.09 N N
39 CAH CAG C C sing 1.53 N N
40 CAH HAH1 C H sing 1.09 N N
41 CAH HAH2 C H sing 1.09 N N
42 CAG CAF C C sing 1.53 N N
43 CAG HAG1 C H sing 1.09 N N
44 CAG HAG2 C H sing 1.09 N N
45 CAF CAE C C sing 1.53 N N
46 CAF HAF1 C H sing 1.09 N N
47 CAF HAF2 C H sing 1.09 N N
48 CAE CAD C C sing 1.51 N N
49 CAE HAE1 C H sing 1.09 N N
50 CAE HAE2 C H sing 1.09 N N
51 CAD OAA C O doub 1.21 N N
52 CAD OAC C O sing 1.34 N N
53 OAC CAB O C sing 1.45 N N
54 CAB CBE C C sing 1.53 N N
55 CAB HAB1 C H sing 1.09 N N
56 CAB HAB2 C H sing 1.09 N N
57 CBE CBK C C sing 1.53 N N
58 CBE OBD C O sing 1.45 N N
59 CBE HBE C H sing 1.09 N N
60 CBK OBL C O sing 1.43 N N
61 CBK HBK1 C H sing 1.09 N N
62 CBK HBK2 C H sing 1.09 N N
63 OBL PBM O P sing 1.61 N N
64 PBM OBU P O doub 1.48 N N
65 PBM OBF P O sing 1.61 N N
66 PBM OBN P O sing 1.61 N N
67 OBF HBF O H sing 0.97 N N
68 OBN CBO O C sing 1.43 N N
69 CBO CBP C C sing 1.53 N N
70 CBO HBO1 C H sing 1.09 N N
71 CBO HBO2 C H sing 1.09 N N
72 CBP OBG C O sing 1.43 N N
73 CBP CBQ C C sing 1.53 N N
74 CBP HBP C H sing 1.09 N N
75 OBG HBG O H sing 0.97 N N
76 CBQ OBR C O sing 1.43 N N
77 CBQ HBQ1 C H sing 1.09 N N
78 CBQ HBQ2 C H sing 1.09 N N
79 OBR HBR O H sing 0.97 N N
80 OBD CBC O C sing 1.34 N N
81 CBC OBJ C O doub 1.21 N N
82 CBC CBB C C sing 1.51 N N
83 CBB CBA C C sing 1.53 N N
84 CBB HBB1 C H sing 1.09 N N
85 CBB HBB2 C H sing 1.09 N N
86 CBA CAZ C C sing 1.53 N N
87 CBA HBA1 C H sing 1.09 N N
88 CBA HBA2 C H sing 1.09 N N
89 CAZ CAY C C sing 1.53 N N
90 CAZ HAZ1 C H sing 1.09 N N
91 CAZ HAZ2 C H sing 1.09 N N
92 CAY CAX C C sing 1.53 N N
93 CAY HAY1 C H sing 1.09 N N
94 CAY HAY2 C H sing 1.09 N N
95 CAX CAW C C sing 1.53 N N
96 CAX HAX1 C H sing 1.09 N N
97 CAX HAX2 C H sing 1.09 N N
98 CAW CAV C C sing 1.53 N N
99 CAW HAW1 C H sing 1.09 N N
100 CAW HAW2 C H sing 1.09 N N
101 CAV CAU C C sing 1.51 N N
102 CAV HAV1 C H sing 1.09 N N
103 CAV HAV2 C H sing 1.09 N N
104 CAU CAT C C doub 1.31 Z N
105 CAU HAU C H sing 1.08 N N
106 CAT CAS C C sing 1.51 N N
107 CAT HAT C H sing 1.08 N N
108 CAS CAR C C sing 1.53 N N
109 CAS HAS1 C H sing 1.09 N N
110 CAS HAS2 C H sing 1.09 N N
111 CAR CBI C C sing 1.53 N N
112 CAR HAR1 C H sing 1.09 N N
113 CAR HAR2 C H sing 1.09 N N
114 CBI CBT C C sing 1.53 N N
115 CBI HBI1 C H sing 1.09 N N
116 CBI HBI2 C H sing 1.09 N N
117 CBT CBW C C sing 1.53 N N
118 CBT HBT1 C H sing 1.09 N N
119 CBT HBT2 C H sing 1.09 N N
120 CBW CBY C C sing 1.53 N N
121 CBW HBW1 C H sing 1.09 N N
122 CBW HBW2 C H sing 1.09 N N
123 CBY HBY1 C H sing 1.09 N N
124 CBY HBY2 C H sing 1.09 N N
125 CBY HBY3 C H sing 1.09 N N



DR9 : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
DR9 1ymt Open in New Window Bound ligand 1 1
DR9 7kc4 Open in New Window Bound ligand 3 1
DR9 7z0s Open in New Window Bound ligand 1 1