Chemical Components in the PDB

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17X : Summary

Code

17X

One-letter code

X

Molecule name

(2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-2-(2-phenyl-1H-benzimidazol-1-yl)-2-(piperidin-4-yl)ethyl 1-(1-benzyl-1H-benzimidazol-2-yl)piperidine-4-carboxylate
OpenEye OEToolkits 1.7.6 [(2S)-2-(2-phenylbenzimidazol-1-yl)-2-piperidin-4-yl-ethyl] 1-[1-(phenylmethyl)benzimidazol-2-yl]piperidine-4-carboxylate

Formula

C40 H42 N6 O2

Formal charge

0

Molecular weight

638.8 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(OCC(n2c3ccccc3nc2c1ccccc1)C4CCNCC4)C8CCN(c5nc7c(n5Cc6ccccc6)cccc7)CC8
SMILES CACTVS 3.370 O=C(OC[CH](C1CCNCC1)n2c3ccccc3nc2c4ccccc4)C5CCN(CC5)c6nc7ccccc7n6Cc8ccccc8
SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)Cn2c3ccccc3nc2N4CCC(CC4)C(=O)OCC(C5CCNCC5)n6c7ccccc7nc6c8ccccc8
Canonical SMILES CACTVS 3.370 O=C(OC[C@H](C1CCNCC1)n2c3ccccc3nc2c4ccccc4)C5CCN(CC5)c6nc7ccccc7n6Cc8ccccc8
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)Cn2c3ccccc3nc2N4CCC(CC4)C(=O)OC[C@H](C5CCNCC5)n6c7ccccc7nc6c8ccccc8

IUPAC InChI

InChI=1S/C40H42N6O2/c47-39(32-21-25-44(26-22-32)40-43-33-15-7-9-17-35(33)45(40)27-29-11-3-1-4-12-29)48-28-37(30-19-23-41-24-20-30)46-36-18-10-8-16-34(36)42-38(46)31-13-5-2-6-14-31/h1-18,30,32,37,41H,19-28H2/t37-/m1/s1

IUPAC InChI key

WDALFJYWTFDSRP-DIPNUNPCSA-N
17X

wwPDB Information

Atom count

90 (48 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-03-26

Last modified at

2013-05-17

Status

Released

Obsoleted

Not Assigned



17X : Atoms of Molecule

Total Number of Atoms: 90
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CAI C CAI N Y N 0 3.895 2.507 -0.32
2 CAJ C CAJ N Y N 0 3.664 3.348 -1.392
3 CAK C CAK N Y N 0 4.728 3.862 -2.109
4 CAL C CAL N Y N 0 6.024 3.535 -1.754
5 CAM C CAM N Y N 0 6.255 2.694 -0.681
6 CAH C CAH N Y N 0 5.19 2.179 0.035
7 CAG C CAG N N N 0 5.442 1.262 1.204
8 NAD N NAD N Y N 0 5.481 -0.126 0.735
9 CAC C CAC N Y N 0 6.597 -0.81 0.284
10 CAF C CAF N Y N 0 7.933 -0.473 0.128
11 CAE C CAE N Y N 0 8.825 -1.407 -0.36
12 CAX C CAX N Y N 0 8.393 -2.681 -0.696
13 CAW C CAW N Y N 0 7.07 -3.033 -0.548
14 CAV C CAV N Y N 0 6.155 -2.1 -0.055
15 NAY N NAY N Y N 0 4.821 -2.144 0.198
16 CAB C CAB N Y N 0 4.423 -0.988 0.668
17 NAA N NAA N N N 0 3.129 -0.683 1.031
18 CAR C CAR N N N 0 2.2 -0.922 -0.081
19 CAQ C CAQ N N N 0 0.801 -0.437 0.308
20 CAN C CAN N N N 0 2.728 -1.432 2.228
21 CAO C CAO N N N 0 1.345 -0.963 2.687
22 CAP C CAP N N N 0 0.335 -1.19 1.558
23 CAS C CAS N N N 0 -1.017 -0.675 1.981
24 OAT O OAT N N N 0 -1.159 -0.177 3.073
25 OAU O OAU N N N 0 -2.062 -0.768 1.145
26 CBP C CBP N N N 0 -3.334 -0.252 1.618
27 CBO C CBO S N N 0 -4.398 -0.445 0.536
28 CBQ C CBQ N N N 0 -4.445 -1.917 0.124
29 CBR C CBR N N N 0 -5.595 -2.136 -0.862
30 CBS C CBS N N N 0 -5.675 -3.621 -1.224
31 NBV N NBV N N N 0 -5.893 -4.412 -0.0060
32 CBT C CBT N N N 0 -4.778 -4.255 0.936
33 CBU C CBU N N N 0 -4.671 -2.789 1.362
34 NBH N NBH N Y N 0 -4.065 0.379 -0.629
35 CBD C CBD N Y N 0 -3.705 -0.08 -1.881
36 CBE C CBE N Y N 0 -3.545 -1.343 -2.435
37 CAZ C CAZ N Y N 0 -3.166 -1.467 -3.755
38 CBA C CBA N Y N 0 -2.944 -0.339 -4.532
39 CBB C CBB N Y N 0 -3.097 0.912 -4.005
40 CBC C CBC N Y N 0 -3.481 1.063 -2.668
41 NBF N NBF N Y N 0 -3.708 2.142 -1.881
42 CBG C CBG N Y N 0 -4.057 1.746 -0.681
43 CBI C CBI N Y N 0 -4.389 2.643 0.447
44 CBJ C CBJ N Y N 0 -3.76 3.883 0.565
45 CBK C CBK N Y N 0 -4.075 4.715 1.62
46 CBL C CBL N Y N 0 -5.011 4.322 2.559
47 CBM C CBM N Y N 0 -5.638 3.094 2.448
48 CBN C CBN N Y N 0 -5.337 2.255 1.395
49 H1 H H1 N N N 0 3.064 2.109 0.243
50 H2 H H2 N N N 0 2.652 3.603 -1.67
51 H3 H H3 N N N 0 4.548 4.519 -2.947
52 H4 H H4 N N N 0 6.855 3.937 -2.314
53 H5 H H5 N N N 0 7.267 2.439 -0.403
54 H6 H H6 N N N 0 6.396 1.515 1.666
55 H7 H H7 N N N 0 4.642 1.376 1.935
56 H8 H H8 N N N 0 8.276 0.518 0.387
57 H9 H H9 N N N 0 9.865 -1.143 -0.482
58 H10 H H10 N N N 0 9.1 -3.403 -1.078
59 H11 H H11 N N N 0 6.741 -4.027 -0.812
60 H12 H H12 N N N 0 2.54 -0.378 -0.962
61 H13 H H13 N N N 0 2.166 -1.988 -0.303
62 H14 H H14 N N N 0 0.831 0.632 0.517
63 H15 H H15 N N N 0 0.109 -0.628 -0.512
64 H16 H H16 N N N 0 2.692 -2.497 1.995
65 H17 H H17 N N N 0 3.452 -1.26 3.025
66 H18 H H18 N N N 0 1.041 -1.531 3.566
67 H19 H H19 N N N 0 1.384 0.098 2.933
68 H20 H H20 N N N 0 0.266 -2.255 1.339
69 H21 H H21 N N N 0 -3.631 -0.788 2.52
70 H22 H H22 N N N 0 -3.233 0.81 1.844
71 H23 H H23 N N N 0 -5.371 -0.146 0.926
72 H24 H H24 N N N 0 -3.502 -2.193 -0.349
73 H25 H H25 N N N 0 -6.533 -1.823 -0.403
74 H26 H H26 N N N 0 -5.418 -1.55 -1.764
75 H27 H H27 N N N 0 -6.503 -3.783 -1.915
76 H28 H H28 N N N 0 -4.742 -3.931 -1.696
77 H29 H H29 N N N 0 -6.044 -5.385 -0.229
78 H31 H H31 N N N 0 -4.953 -4.876 1.814
79 H32 H H32 N N N 0 -3.849 -4.561 0.454
80 H33 H H33 N N N 0 -3.834 -2.67 2.049
81 H34 H H34 N N N 0 -5.594 -2.486 1.857
82 H35 H H35 N N N 0 -3.716 -2.224 -1.834
83 H36 H H36 N N N 0 -3.041 -2.449 -4.187
84 H37 H H37 N N N 0 -2.647 -0.451 -5.564
85 H38 H H38 N N N 0 -2.921 1.783 -4.619
86 H39 H H39 N N N 0 -3.029 4.191 -0.167
87 H40 H H40 N N N 0 -3.589 5.675 1.713
88 H41 H H41 N N N 0 -5.254 4.977 3.383
89 H42 H H42 N N N 0 -6.368 2.792 3.185
90 H43 H H43 N N N 0 -5.83 1.298 1.307



17X : Chemical Bonds

Total Number of Bonds: 97
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAW CAX C C doub 1.377003 N Y
2 CAW CAV C C sing 1.3966972 N Y
3 CAX CAE C C sing 1.3865771 N Y
4 NAY CAV N C sing 1.3584921 N Y
5 NAY CAB N C doub 1.3098245 N Y
6 CAV CAC C C doub 1.4051281 N Y
7 CAN CAO C C sing 1.5307943 N N
8 CAN NAA C N sing 1.4678593 N N
9 CAE CAF C C doub 1.380639 N Y
10 CAO CAP C C sing 1.5317539 N N
11 CAB NAA C N sing 1.3781255 N N
12 CAB NAD C N sing 1.3663445 N Y
13 NAA CAR N C sing 1.4685727 N N
14 CBT CBU C C sing 1.5303859 N N
15 CBT NBV C N sing 1.4680729 N N
16 CAC CAF C C sing 1.386651 N Y
17 CAC NAD C N sing 1.384454 N Y
18 CBU CBQ C C sing 1.5310467 N N
19 CAP CAS C C sing 1.5073347 N N
20 CAP CAQ C C sing 1.5318829 N N
21 NAD CAG N C sing 1.4656146 N N
22 OAU CBP O C sing 1.4518846 N N
23 OAU CAS O C sing 1.3414805 N N
24 CAR CAQ C C sing 1.5309302 N N
25 CBP CBO C C sing 1.5297284 N N
26 NBV CBS N C sing 1.4685806 N N
27 CAS OAT C O doub 1.2085661 N N
28 CBQ CBO C C sing 1.529293 N N
29 CBQ CBR C C sing 1.5305741 N N
30 CBS CBR C C sing 1.530578 N N
31 CBO NBH C N sing 1.4652952 N N
32 CAG CAH C C sing 1.5069685 N N
33 CAI CAH C C doub 1.3822569 N Y
34 CAI CAJ C C sing 1.3819646 N Y
35 CBE CAZ C C doub 1.3789188 N Y
36 CBE CBD C C sing 1.3884109 N Y
37 CAZ CBA C C sing 1.3875867 N Y
38 CAH CAM C C sing 1.3827893 N Y
39 CAJ CAK C C doub 1.3821653 N Y
40 NBH CBD N C sing 1.381226 N Y
41 NBH CBG N C sing 1.3680121 N Y
42 CBD CBC C C doub 1.4057006 N Y
43 CBA CBB C C doub 1.3660669 N Y
44 CAM CAL C C doub 1.3827404 N Y
45 CAK CAL C C sing 1.382957 N Y
46 CBC CBB C C sing 1.3992233 N Y
47 CBC NBF C N sing 1.354673 N Y
48 CBG CBI C C sing 1.4789243 N N
49 CBG NBF C N doub 1.3109603 N Y
50 CBN CBI C C doub 1.3956906 N Y
51 CBN CBM C C sing 1.3796127 N Y
52 CBI CBJ C C sing 1.3954085 N Y
53 CBM CBL C C doub 1.3832693 N Y
54 CBJ CBK C C doub 1.3800268 N Y
55 CBL CBK C C sing 1.3828471 N Y
56 CAI H1 C H sing 1.0797843 N N
57 CAJ H2 C H sing 1.0800245 N N
58 CAK H3 C H sing 1.0799505 N N
59 CAL H4 C H sing 1.079706 N N
60 CAM H5 C H sing 1.0800245 N N
61 CAG H6 C H sing 1.0897564 N N
62 CAG H7 C H sing 1.0896591 N N
63 CAF H8 C H sing 1.0801903 N N
64 CAE H9 C H sing 1.0798981 N N
65 CAX H10 C H sing 1.0803041 N N
66 CAW H11 C H sing 1.0798023 N N
67 CAR H12 C H sing 1.0898151 N N
68 CAR H13 C H sing 1.0894017 N N
69 CAQ H14 C H sing 1.0896522 N N
70 CAQ H15 C H sing 1.0898372 N N
71 CAN H16 C H sing 1.0907841 N N
72 CAN H17 C H sing 1.0903986 N N
73 CAO H18 C H sing 1.0898077 N N
74 CAO H19 C H sing 1.0898432 N N
75 CAP H20 C H sing 1.089471 N N
76 CBP H21 C H sing 1.0904628 N N
77 CBP H22 C H sing 1.0904683 N N
78 CBO H23 C H sing 1.0900596 N N
79 CBQ H24 C H sing 1.0904834 N N
80 CBR H25 C H sing 1.0901808 N N
81 CBR H26 C H sing 1.090105 N N
82 CBS H27 C H sing 1.0905545 N N
83 CBS H28 C H sing 1.0905838 N N
84 NBV H29 N H sing 1.0095836 N N
85 CBT H31 C H sing 1.0895641 N N
86 CBT H32 C H sing 1.0904132 N N
87 CBU H33 C H sing 1.0893571 N N
88 CBU H34 C H sing 1.0903041 N N
89 CBE H35 C H sing 1.080094 N N
90 CAZ H36 C H sing 1.08008 N N
91 CBA H37 C H sing 1.0797116 N N
92 CBB H38 C H sing 1.0800986 N N
93 CBJ H39 C H sing 1.0793743 N N
94 CBK H40 C H sing 1.0800208 N N
95 CBL H41 C H sing 1.0803009 N N
96 CBM H42 C H sing 1.080404 N N
97 CBN H43 C H sing 1.080112 N N



17X : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
17X 4jvf Open in New Window Bound ligand 1 1