Chemical Components in the PDB

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1RD : Summary

Code

1RD

One-letter code

X

Molecule name

N~2~-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-N-(4-{[(1,3-thiazol-5-ylmethoxy)carbonyl]amino}butyl)-L-valinamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N~2~-(methyl{[2-(propan-2-yl)-1,3-thiazol-4-yl]methyl}carbamoyl)-N-(4-{[(1,3-thiazol-5-ylmethoxy)carbonyl]amino}butyl)-L-valinamide
OpenEye OEToolkits 1.7.6 1,3-thiazol-5-ylmethyl N-[4-[[(2S)-3-methyl-2-[[methyl-[(2-propan-2-yl-1,3-thiazol-4-yl)methyl]carbamoyl]amino]butanoyl]amino]butyl]carbamate

Formula

C23 H36 N6 O4 S2

Formal charge

0

Molecular weight

524.7 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(OCc1scnc1)NCCCCNC(=O)C(NC(=O)N(Cc2nc(sc2)C(C)C)C)C(C)C
SMILES CACTVS 3.370 CC(C)[CH](NC(=O)N(C)Cc1csc(n1)C(C)C)C(=O)NCCCCNC(=O)OCc2scnc2
SMILES OpenEye OEToolkits 1.7.6 CC(C)c1nc(cs1)CN(C)C(=O)NC(C(C)C)C(=O)NCCCCNC(=O)OCc2cncs2
Canonical SMILES CACTVS 3.370 CC(C)[C@H](NC(=O)N(C)Cc1csc(n1)C(C)C)C(=O)NCCCCNC(=O)OCc2scnc2
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(C)c1nc(cs1)CN(C)C(=O)N[C@@H](C(C)C)C(=O)NCCCCNC(=O)OCc2cncs2

IUPAC InChI

InChI=1S/C23H36N6O4S2/c1-15(2)19(28-22(31)29(5)11-17-13-34-21(27-17)16(3)4)20(30)25-8-6-7-9-26-23(32)33-12-18-10-24-14-35-18/h10,13-16,19H,6-9,11-12H2,1-5H3,(H,25,30)(H,26,32)(H,28,31)/t19-/m0/s1

IUPAC InChI key

OWSUPSVMUSHQHC-IBGZPJMESA-N
1RD

wwPDB Information

Atom count

71 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-05-06

Last modified at

2013-06-14

Status

Released

Obsoleted

Not Assigned



1RD : Atoms of Molecule

Total Number of Atoms: 71
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C01 N N N 0 -8.093 4.237 1.831
2 C02 C C02 N N N 0 -6.87 3.446 1.363
3 C03 C C03 N N N 0 -5.854 4.403 0.735
4 C04 C C04 N Y N 0 -7.294 2.423 0.341
5 C06 C C06 N Y N 0 -7.564 0.392 -0.527
6 C07 C C07 N N N 0 -7.44 -1.11 -0.519
7 C09 C C09 N N N 0 -5.916 -1.73 -2.451
8 C10 C C10 N N N 0 -5.087 -1.629 -0.162
9 C13 C C13 S N N 0 -2.749 -2.13 0.31
10 C14 C C14 N N N 0 -1.452 -1.916 -0.427
11 C17 C C17 N N N 0 0.915 -1.339 -0.459
12 C18 C C18 N N N 0 1.964 -0.783 0.506
13 C19 C C19 N N N 0 3.31 -0.67 -0.214
14 C20 C C20 N N N 0 4.359 -0.115 0.75
15 C22 C C22 N N N 0 6.726 0.463 0.718
16 C25 C C25 N N N 0 9.031 1.065 0.858
17 C26 C C26 N Y N 0 10.264 1.1 -0.0090
18 C27 C C27 N Y N 0 10.66 2.123 -0.773
19 C29 C C29 N Y N 0 12.342 0.759 -1.282
20 C31 C C31 N N N 0 -2.768 -3.537 0.912
21 C32 C C32 N N N 0 -4.106 -3.772 1.617
22 C33 C C33 N N N 0 -1.628 -3.674 1.922
23 C34 C C34 N Y N 0 -8.115 1.066 -1.541
24 H1 H H1 N N N 0 8.805 2.072 1.207
25 H10 H H10 N N N 0 2.065 -1.454 1.359
26 H11 H H11 N N N 0 1.654 0.202 0.853
27 H12 H H12 N N N 0 0.814 -0.668 -1.312
28 H13 H H13 N N N 0 1.225 -2.324 -0.806
29 H14 H H14 N N N 0 -0.449 -1.182 1.161
30 H15 H H15 N N N 0 -2.84 -1.393 1.107
31 H16 H H16 N N N 0 -2.642 -4.273 0.118
32 H17 H H17 N N N 0 -1.692 -2.871 2.655
33 H18 H H18 N N N 0 -1.706 -4.636 2.429
34 H19 H H19 N N N 0 -0.672 -3.615 1.401
35 H2 H H2 N N N 0 9.208 0.414 1.714
36 H20 H H20 N N N 0 -4.918 -3.673 0.898
37 H21 H H21 N N N 0 -4.119 -4.774 2.046
38 H22 H H22 N N N 0 -4.232 -3.035 2.411
39 H23 H H23 N N N 0 -3.737 -2.139 -1.57
40 H24 H H24 N N N 0 -5.628 -0.798 -2.936
41 H25 H H25 N N N 0 -5.129 -2.471 -2.589
42 H26 H H26 N N N 0 -6.843 -2.098 -2.892
43 H27 H H27 N N N 0 -8.21 -1.541 -1.159
44 H28 H H28 N N N 0 -7.565 -1.479 0.499
45 H29 H H29 N N N 0 -8.527 0.636 -2.442
46 H3 H H3 N N N 0 13.257 0.45 -1.766
47 H30 H H30 N N N 0 -6.415 2.942 2.215
48 H31 H H31 N N N 0 -6.309 4.908 -0.117
49 H32 H H32 N N N 0 -5.548 5.144 1.474
50 H33 H H33 N N N 0 -4.983 3.84 0.402
51 H34 H H34 N N N 0 -7.787 4.977 2.57
52 H35 H H35 N N N 0 -8.548 4.741 0.979
53 H36 H H36 N N N 0 -8.817 3.555 2.278
54 H4 H H4 N N N 0 10.109 3.05 -0.839
55 H5 H H5 N N N 0 5.723 -0.271 -0.869
56 H6 H H6 N N N 0 4.46 -0.785 1.603
57 H7 H H7 N N N 0 4.049 0.871 1.097
58 H8 H H8 N N N 0 3.209 0.0010 -1.068
59 H9 H H9 N N N 0 3.62 -1.655 -0.562
60 N05 N N05 N Y N 0 -7.133 1.148 0.462
61 N08 N N08 N N N 0 -6.118 -1.494 -1.019
62 N12 N N12 N N N 0 -3.87 -1.983 -0.622
63 N16 N N16 N N N 0 -0.373 -1.448 0.231
64 N21 N N21 N N N 0 5.647 -0.0060 0.06
65 N28 N N28 N Y N 0 11.778 1.909 -1.436
66 O11 O O11 N N N 0 -5.254 -1.433 1.026
67 O15 O O15 N N N 0 -1.379 -2.166 -1.611
68 O23 O O23 N N N 0 6.631 0.795 1.883
69 O24 O O24 N N N 0 7.911 0.558 0.086
70 S30 S S30 N Y N 0 11.434 -0.204 -0.2
71 S35 S S35 N Y N 0 -8.05 2.783 -1.149



1RD : Chemical Bonds

Total Number of Bonds: 72
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 S35 C34 S C sing 1.7623785 N Y
2 S35 C04 S C sing 1.7091624 N Y
3 C34 C06 C C doub 1.3364404 N Y
4 C09 N08 C N sing 1.4653068 N N
5 C02 C04 C C sing 1.5069138 N N
6 C02 C03 C C sing 1.5305192 N N
7 C02 C01 C C sing 1.5298477 N N
8 C04 N05 C N doub 1.2908087 N Y
9 C06 N05 C N sing 1.3173527 N Y
10 C06 C07 C C sing 1.5071311 N N
11 N08 C07 N C sing 1.4646297 N N
12 N08 C10 N C sing 1.347455 N N
13 O11 C10 O C doub 1.2155858 N N
14 O15 C14 O C doub 1.2123057 N N
15 C10 N12 C N sing 1.3483342 N N
16 C17 N16 C N sing 1.4652389 N N
17 C17 C18 C C sing 1.5299549 N N
18 N12 C13 N C sing 1.4652215 N N
19 C14 N16 C N sing 1.3476754 N N
20 C14 C13 C C sing 1.5070415 N N
21 C18 C19 C C sing 1.5306486 N N
22 C13 C31 C C sing 1.5304947 N N
23 O23 C22 O C doub 1.2151024 N N
24 C25 O24 C O sing 1.4517001 N N
25 C25 C26 C C sing 1.5077145 N N
26 C32 C31 C C sing 1.5305208 N N
27 C19 C20 C C sing 1.5289611 N N
28 C31 C33 C C sing 1.5292053 N N
29 C22 O24 C O sing 1.3463558 N N
30 C22 N21 C N sing 1.3480229 N N
31 C27 C26 C C doub 1.3368025 N Y
32 C27 N28 C N sing 1.3173037 N Y
33 C26 S30 C S sing 1.7623272 N Y
34 C20 N21 C N sing 1.4652389 N N
35 N28 C29 N C doub 1.2900822 N Y
36 S30 C29 S C sing 1.7095487 N Y
37 C25 H1 C H sing 1.0894613 N N
38 C25 H2 C H sing 1.0898926 N N
39 C29 H3 C H sing 1.0802602 N N
40 C27 H4 C H sing 1.0804101 N N
41 N21 H5 N H sing 0.9690418 N N
42 C20 H6 C H sing 1.0893621 N N
43 C20 H7 C H sing 1.0902774 N N
44 C19 H8 C H sing 1.0907602 N N
45 C19 H9 C H sing 1.0896921 N N
46 C18 H10 C H sing 1.0899775 N N
47 C18 H11 C H sing 1.0893732 N N
48 C17 H12 C H sing 1.0899775 N N
49 C17 H13 C H sing 1.0893732 N N
50 N16 H14 N H sing 0.9702742 N N
51 C13 H15 C H sing 1.0893388 N N
52 C31 H16 C H sing 1.0899578 N N
53 C33 H17 C H sing 1.0891254 N N
54 C33 H18 C H sing 1.0902188 N N
55 C33 H19 C H sing 1.0903476 N N
56 C32 H20 C H sing 1.089085 N N
57 C32 H21 C H sing 1.0900522 N N
58 C32 H22 C H sing 1.0906333 N N
59 N12 H23 N H sing 0.9699119 N N
60 C09 H24 C H sing 1.0894003 N N
61 C09 H25 C H sing 1.089722 N N
62 C09 H26 C H sing 1.09052 N N
63 C07 H27 C H sing 1.0900738 N N
64 C07 H28 C H sing 1.0900046 N N
65 C34 H29 C H sing 1.0800208 N N
66 C02 H30 C H sing 1.08947 N N
67 C03 H31 C H sing 1.089933 N N
68 C03 H32 C H sing 1.0903385 N N
69 C03 H33 C H sing 1.0892653 N N
70 C01 H34 C H sing 1.0896591 N N
71 C01 H35 C H sing 1.08947 N N
72 C01 H36 C H sing 1.0904628 N N



1RD : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
1RD 4k9t Open in New Window Bound ligand 2 1