Chemical Components in the PDB

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0DX : Summary

Code

0DX

One-letter code

X

Molecule name

4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}-2,7-bis[3-(morpholin-4-yl)propyl]benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone

Systematic names

ProgramVersionName
ACDLabs 12.01 4,9-bis{[3-(4-methylpiperazin-1-yl)propyl]amino}-2,7-bis[3-(morpholin-4-yl)propyl]benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone

Formula

C44 H66 N10 O6

Formal charge

0

Molecular weight

831.058 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C6c2c5c3c(c(NCCCN1CCN(C)CC1)c2)C(=O)N(C(=O)c3cc(NCCCN4CCN(C)CC4)c5C(=O)N6CCCN7CCOCC7)CCCN8CCOCC8
SMILES CACTVS 3.370 CN1CCN(CCCNc2cc3C(=O)N(CCCN4CCOCC4)C(=O)c5c(NCCCN6CCN(C)CC6)cc7C(=O)N(CCCN8CCOCC8)C(=O)c2c7c35)CC1
SMILES OpenEye OEToolkits 1.7.6 CN1CCN(CC1)CCCNc2cc3c4c5c2C(=O)N(C(=O)c5cc(c4C(=O)N(C3=O)CCCN6CCOCC6)NCCCN7CCN(CC7)C)CCCN8CCOCC8
Canonical SMILES CACTVS 3.370 CN1CCN(CCCNc2cc3C(=O)N(CCCN4CCOCC4)C(=O)c5c(NCCCN6CCN(C)CC6)cc7C(=O)N(CCCN8CCOCC8)C(=O)c2c7c35)CC1
Canonical SMILES OpenEye OEToolkits 1.7.6 CN1CCN(CC1)CCCNc2cc3c4c5c2C(=O)N(C(=O)c5cc(c4C(=O)N(C3=O)CCCN6CCOCC6)NCCCN7CCN(CC7)C)CCCN8CCOCC8

IUPAC InChI

InChI=1S/C44H66N10O6/c1-47-15-19-49(20-16-47)9-3-7-45-35-31-33-38-37-34(42(56)53(43(57)39(35)37)13-5-11-51-23-27-59-28-24-51)32-36(46-8-4-10-50-21-17-48(2)18-22-50)40(38)44(58)54(41(33)55)14-6-12-52-25-29-60-30-26-52/h31-32,45-46H,3-30H2,1-2H3

IUPAC InChI key

JOVJRDSWNCUWBX-UHFFFAOYSA-N
0DX

wwPDB Information

Atom count

126 (60 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-12-19

Last modified at

2012-12-28

Status

Released

Obsoleted

Not Assigned



0DX : 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 CAA C CAA N N N 0 12.278 -3.182 0.481
2 CAB C CAB N N N 0 -12.039 3.906 1.066
3 OAE O OAE N N N 0 -0.0010 3.856 -1.529
4 OAF O OAF N N N 0 -0.04 -3.982 1.267
5 OAG O OAG N N N 0 3.704 1.441 -1.19
6 OAH O OAH N N N 0 -3.739 -1.552 0.966
7 CAI C CAI N Y N 0 -1.664 1.804 -0.537
8 CAJ C CAJ N Y N 0 1.625 -1.925 0.287
9 CAK C CAK N N N 0 5.925 -2.066 -0.151
10 CAL C CAL N N N 0 -5.958 1.96 -0.054
11 CAM C CAM N N N 0 3.113 4.649 -0.739
12 CAN C CAN N N N 0 -3.153 -4.769 0.473
13 CAO C CAO N N N 0 4.425 -2.18 0.129
14 CAP C CAP N N N 0 -4.461 2.068 -0.351
15 CAQ C CAQ N N N 0 6.633 -3.328 0.344
16 CAR C CAR N N N 0 -6.668 3.224 -0.544
17 CAS C CAS N N N 0 3.928 5.823 -1.285
18 CAT C CAT N N N 0 -3.969 -5.945 1.014
19 CAU C CAU N N N 0 10.233 -4.365 -0.051
20 CAV C CAV N N N 0 10.158 -2.011 0.509
21 CAW C CAW N N N 0 -9.854 2.931 1.443
22 CAX C CAX N N N 0 -10.35 4.009 -0.667
23 CAY C CAY N N N 0 5.858 8.472 0.573
24 CAZ C CAZ N N N 0 3.765 8.131 1.687
25 CBA C CBA N N N 0 -5.898 -8.585 -0.857
26 CBB C CBB N N N 0 -3.804 -8.24 -1.968
27 CBC C CBC N N N 0 8.753 -4.499 0.316
28 CBD C CBD N N N 0 8.679 -2.145 0.876
29 CBE C CBE N N N 0 -8.357 3.121 1.188
30 CBF C CBF N N N 0 -8.853 4.198 -0.922
31 CBG C CBG N N N 0 5.364 7.66 -0.628
32 CBH C CBH N N N 0 3.25 7.315 0.498
33 CBI C CBI N N N 0 -5.405 -7.778 0.347
34 CBJ C CBJ N N N 0 -3.29 -7.43 -0.775
35 CBK C CBK N N N 0 2.636 3.775 -1.9
36 CBL C CBL N N N 0 -2.677 -3.9 1.639
37 NBM N NBM N N N 0 3.746 -0.971 -0.345
38 NBN N NBN N N N 0 -3.782 0.858 0.119
39 CBO C CBO N Y N 0 2.375 -0.844 -0.199
40 CBP C CBP N Y N 0 -2.413 0.726 -0.042
41 CBQ C CBQ N N N 0 0.525 2.803 -1.229
42 CBR C CBR N N N 0 -0.565 -2.926 0.973
43 CBS C CBS N N N 0 2.499 1.515 -1.048
44 CBT C CBT N N N 0 -2.536 -1.631 0.812
45 CBU C CBU N Y N 0 -0.295 1.694 -0.706
46 CBV C CBV N Y N 0 0.256 -1.816 0.455
47 CBW C CBW N Y N 0 1.751 0.358 -0.536
48 CBX C CBX N Y N 0 -1.789 -0.477 0.291
49 CBY C CBY N Y N 0 0.353 0.481 -0.368
50 CBZ C CBZ N Y N 0 -0.391 -0.6 0.123
51 NCA N NCA N N N 0 10.838 -3.292 0.75
52 NCB N NCB N N N 0 -10.601 4.01 0.781
53 OCC O OCC N N N 0 4.738 9.073 1.228
54 OCD O OCD N N N 0 -4.777 -9.184 -1.514
55 NCE N NCE N N N 0 8.073 -3.219 0.075
56 NCF N NCF N N N 0 -8.105 3.12 -0.26
57 NCG N NCG N N N 0 4.386 6.662 -0.17
58 NCH N NCH N N N 0 -4.426 -6.78 -0.106
59 NCI N NCI N N N 0 1.855 2.651 -1.377
60 NCJ N NCJ N N N 0 -1.895 -2.774 1.121
61 HAA H HAA N N N 0 12.435 -2.961 -0.574
62 HAAA H HAAA N N N 0 12.701 -2.381 1.087
63 HAAB H HAAB N N N 0 12.767 -4.124 0.732
64 HAB H HAB N N N 0 -12.427 2.978 0.644
65 HABA H HABA N N N 0 -12.197 3.908 2.144
66 HABB H HABB N N N 0 -12.56 4.753 0.62
67 HAI H HAI N N N 0 -2.161 2.727 -0.794
68 HAJ H HAJ N N N 0 2.122 -2.849 0.542
69 HAK H HAK N N N 0 6.087 -1.955 -1.223
70 HAKA H HAKA N N N 0 6.326 -1.196 0.369
71 HAL H HAL N N N 0 -6.369 1.091 -0.568
72 HALA H HALA N N N 0 -6.109 1.852 1.02
73 HAM H HAM N N N 0 3.734 4.056 -0.068
74 HAMA H HAMA N N N 0 2.249 5.03 -0.193
75 HAN H HAN N N N 0 -2.289 -5.148 -0.074
76 HANA H HANA N N N 0 -3.773 -4.173 -0.196
77 HAO H HAO N N N 0 4.023 -3.049 -0.391
78 HAOA H HAOA N N N 0 4.263 -2.291 1.201
79 HAP H HAP N N N 0 -4.31 2.176 -1.425
80 HAPA H HAPA N N N 0 -4.051 2.938 0.163
81 HAQ H HAQ N N N 0 6.471 -3.439 1.416
82 HAQA H HAQA N N N 0 6.232 -4.198 -0.176
83 HAR H HAR N N N 0 -6.258 4.093 -0.03
84 HARA H HARA N N N 0 -6.517 3.332 -1.618
85 HAS H HAS N N N 0 4.792 5.442 -1.831
86 HASA H HASA N N N 0 3.307 6.416 -1.956
87 HAT H HAT N N N 0 -3.349 -6.541 1.682
88 HATA H HATA N N N 0 -4.833 -5.566 1.56
89 HAU H HAU N N N 0 10.745 -5.305 0.155
90 HAUA H HAUA N N N 0 10.325 -4.125 -1.11
91 HAV H HAV N N N 0 10.25 -1.744 -0.544
92 HAVA H HAVA N N N 0 10.616 -1.235 1.122
93 HAW H HAW N N N 0 -10.172 1.969 1.042
94 HAWA H HAWA N N N 0 -10.047 2.96 2.516
95 HAX H HAX N N N 0 -10.904 4.824 -1.132
96 HAXA H HAXA N N N 0 -10.674 3.059 -1.092
97 HAY H HAY N N N 0 6.376 7.813 1.269
98 HAYA H HAYA N N N 0 6.54 9.249 0.231
99 HAZ H HAZ N N N 0 2.934 8.662 2.151
100 HAZA H HAZA N N N 0 4.222 7.463 2.417
101 HBA H HBA N N N 0 -6.581 -9.364 -0.519
102 HBAA H HBAA N N N 0 -6.415 -7.923 -1.551
103 HBB H HBB N N N 0 -4.26 -7.568 -2.695
104 HBBA H HBBA N N N 0 -2.973 -8.769 -2.434
105 HBC H HBC N N N 0 8.295 -5.275 -0.297
106 HBCA H HBCA N N N 0 8.662 -4.766 1.369
107 HBD H HBD N N N 0 8.587 -2.386 1.935
108 HBDA H HBDA N N N 0 8.167 -1.205 0.67
109 HBE H HBE N N N 0 -8.033 4.07 1.613
110 HBEA H HBEA N N N 0 -7.803 2.306 1.654
111 HBF H HBF N N N 0 -8.66 4.169 -1.994
112 HBFA H HBFA N N N 0 -8.534 5.161 -0.521
113 HBG H HBG N N N 0 4.893 8.327 -1.35
114 HBGA H HBGA N N N 0 6.208 7.154 -1.097
115 HBH H HBH N N N 0 2.551 6.558 0.851
116 HBHA H HBHA N N N 0 2.745 7.977 -0.205
117 HBI H HBI N N N 0 -6.249 -7.273 0.817
118 HBIA H HBIA N N N 0 -4.935 -8.449 1.067
119 HBJ H HBJ N N N 0 -2.786 -8.095 -0.074
120 HBJA H HBJA N N N 0 -2.59 -6.672 -1.125
121 HBK H HBK N N N 0 2.015 4.368 -2.571
122 HBKA H HBKA N N N 0 3.5 3.394 -2.446
123 HBL H HBL N N N 0 -3.541 -3.521 2.185
124 HBLA H HBLA N N N 0 -2.057 -4.496 2.307
125 HNBM H HNBM N N N 0 4.258 -0.259 -0.761
126 HNBN H HNBN N N N 0 -4.291 0.149 0.542



0DX : Chemical Bonds

Total Number of Bonds: 133
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 NCA CAA N C sing 1.47 N N
2 CAA HAA C H sing 1.09 N N
3 CAA HAAA C H sing 1.09 N N
4 CAA HAAB C H sing 1.09 N N
5 CAB NCB C N sing 1.47 N N
6 CAB HAB C H sing 1.09 N N
7 CAB HABA C H sing 1.09 N N
8 CAB HABB C H sing 1.09 N N
9 OAE CBQ O C doub 1.21 N N
10 CBR OAF C O doub 1.22 N N
11 CBS OAG C O doub 1.22 N N
12 OAH CBT O C doub 1.22 N N
13 CBP CAI C C doub 1.4 N Y
14 CAI CBU C C sing 1.38 N Y
15 CAI HAI C H sing 1.08 N N
16 CBV CAJ C C doub 1.38 N Y
17 CAJ CBO C C sing 1.4 N Y
18 CAJ HAJ C H sing 1.08 N N
19 CAO CAK C C sing 1.53 N N
20 CAK CAQ C C sing 1.53 N N
21 CAK HAK C H sing 1.09 N N
22 CAK HAKA C H sing 1.09 N N
23 CAR CAL C C sing 1.53 N N
24 CAL CAP C C sing 1.53 N N
25 CAL HAL C H sing 1.09 N N
26 CAL HALA C H sing 1.09 N N
27 CBK CAM C C sing 1.53 N N
28 CAM CAS C C sing 1.53 N N
29 CAM HAM C H sing 1.09 N N
30 CAM HAMA C H sing 1.09 N N
31 CAN CAT C C sing 1.53 N N
32 CAN CBL C C sing 1.53 N N
33 CAN HAN C H sing 1.09 N N
34 CAN HANA C H sing 1.09 N N
35 NBM CAO N C sing 1.47 N N
36 CAO HAO C H sing 1.09 N N
37 CAO HAOA C H sing 1.09 N N
38 CAP NBN C N sing 1.46 N N
39 CAP HAP C H sing 1.09 N N
40 CAP HAPA C H sing 1.09 N N
41 CAQ NCE C N sing 1.47 N N
42 CAQ HAQ C H sing 1.09 N N
43 CAQ HAQA C H sing 1.09 N N
44 NCF CAR N C sing 1.47 N N
45 CAR HAR C H sing 1.09 N N
46 CAR HARA C H sing 1.09 N N
47 CAS NCG C N sing 1.47 N N
48 CAS HAS C H sing 1.09 N N
49 CAS HASA C H sing 1.09 N N
50 NCH CAT N C sing 1.47 N N
51 CAT HAT C H sing 1.09 N N
52 CAT HATA C H sing 1.09 N N
53 CBC CAU C C sing 1.53 N N
54 CAU NCA C N sing 1.47 N N
55 CAU HAU C H sing 1.09 N N
56 CAU HAUA C H sing 1.09 N N
57 CBD CAV C C sing 1.53 N N
58 NCA CAV N C sing 1.47 N N
59 CAV HAV C H sing 1.09 N N
60 CAV HAVA C H sing 1.09 N N
61 NCB CAW N C sing 1.47 N N
62 CAW CBE C C sing 1.53 N N
63 CAW HAW C H sing 1.09 N N
64 CAW HAWA C H sing 1.09 N N
65 CAX NCB C N sing 1.47 N N
66 CAX CBF C C sing 1.53 N N
67 CAX HAX C H sing 1.09 N N
68 CAX HAXA C H sing 1.09 N N
69 CBG CAY C C sing 1.53 N N
70 CAY OCC C O sing 1.43 N N
71 CAY HAY C H sing 1.09 N N
72 CAY HAYA C H sing 1.09 N N
73 CBH CAZ C C sing 1.53 N N
74 CAZ OCC C O sing 1.43 N N
75 CAZ HAZ C H sing 1.09 N N
76 CAZ HAZA C H sing 1.09 N N
77 CBA CBI C C sing 1.53 N N
78 CBA OCD C O sing 1.43 N N
79 CBA HBA C H sing 1.09 N N
80 CBA HBAA C H sing 1.09 N N
81 OCD CBB O C sing 1.43 N N
82 CBB CBJ C C sing 1.53 N N
83 CBB HBB C H sing 1.09 N N
84 CBB HBBA C H sing 1.09 N N
85 CBC NCE C N sing 1.47 N N
86 CBC HBC C H sing 1.09 N N
87 CBC HBCA C H sing 1.09 N N
88 NCE CBD N C sing 1.47 N N
89 CBD HBD C H sing 1.09 N N
90 CBD HBDA C H sing 1.09 N N
91 NCF CBE N C sing 1.47 N N
92 CBE HBE C H sing 1.09 N N
93 CBE HBEA C H sing 1.09 N N
94 CBF NCF C N sing 1.47 N N
95 CBF HBF C H sing 1.09 N N
96 CBF HBFA C H sing 1.09 N N
97 NCG CBG N C sing 1.47 N N
98 CBG HBG C H sing 1.09 N N
99 CBG HBGA C H sing 1.09 N N
100 NCG CBH N C sing 1.47 N N
101 CBH HBH C H sing 1.09 N N
102 CBH HBHA C H sing 1.09 N N
103 CBI NCH C N sing 1.47 N N
104 CBI HBI C H sing 1.09 N N
105 CBI HBIA C H sing 1.09 N N
106 NCH CBJ N C sing 1.47 N N
107 CBJ HBJ C H sing 1.09 N N
108 CBJ HBJA C H sing 1.09 N N
109 NCI CBK N C sing 1.47 N N
110 CBK HBK C H sing 1.09 N N
111 CBK HBKA C H sing 1.09 N N
112 NCJ CBL N C sing 1.47 N N
113 CBL HBL C H sing 1.09 N N
114 CBL HBLA C H sing 1.09 N N
115 CBO NBM C N sing 1.38 N N
116 NBM HNBM N H sing 0.97 N N
117 NBN CBP N C sing 1.38 N N
118 NBN HNBN N H sing 0.97 N N
119 CBW CBO C C doub 1.4 N Y
120 CBP CBX C C sing 1.4 N Y
121 CBU CBQ C C sing 1.48 N N
122 CBQ NCI C N sing 1.35 N N
123 NCJ CBR N C sing 1.35 N N
124 CBR CBV C C sing 1.47 N N
125 NCI CBS N C sing 1.35 N N
126 CBW CBS C C sing 1.47 N N
127 CBT CBX C C sing 1.47 N N
128 CBT NCJ C N sing 1.35 N N
129 CBU CBY C C doub 1.42 N Y
130 CBZ CBV C C sing 1.42 N Y
131 CBY CBW C C sing 1.41 N Y
132 CBX CBZ C C doub 1.41 N Y
133 CBZ CBY C C sing 1.4 N Y



0DX : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
0DX 3uyh Open in New Window Bound ligand 1 1
0DX 4da3 Open in New Window Bound ligand 1 1