Chemical Components in the PDB

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1RH : Summary

Code

1RH

One-letter code

X

Molecule name

N-{(3S)-5-(4-aminobenzoyl)-1-[(2-methoxynaphthalen-1-yl)methyl]-2-oxo-2,3,4,5-tetrahydro-1H-1,5-benzodiazepin-3-yl}-N~2~-methyl-L-alaninamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-{(3S)-5-(4-aminobenzoyl)-1-[(2-methoxynaphthalen-1-yl)methyl]-2-oxo-2,3,4,5-tetrahydro-1H-1,5-benzodiazepin-3-yl}-N~2~-methyl-L-alaninamide
OpenEye OEToolkits 1.7.6 (2S)-N-[(3S)-1-(4-aminophenyl)carbonyl-5-[(2-methoxynaphthalen-1-yl)methyl]-4-oxidanylidene-2,3-dihydro-1,5-benzodiazepin-3-yl]-2-(methylamino)propanamide

Formula

C32 H33 N5 O4

Formal charge

0

Molecular weight

551.636 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(N2c1c(cccc1)N(C(=O)C(NC(=O)C(NC)C)C2)Cc4c3ccccc3ccc4OC)c5ccc(N)cc5
SMILES CACTVS 3.370 CN[CH](C)C(=O)N[CH]1CN(C(=O)c2ccc(N)cc2)c3ccccc3N(Cc4c(OC)ccc5ccccc45)C1=O
SMILES OpenEye OEToolkits 1.7.6 CC(C(=O)NC1CN(c2ccccc2N(C1=O)Cc3c4ccccc4ccc3OC)C(=O)c5ccc(cc5)N)NC
Canonical SMILES CACTVS 3.370 CN[C@@H](C)C(=O)N[C@H]1CN(C(=O)c2ccc(N)cc2)c3ccccc3N(Cc4c(OC)ccc5ccccc45)C1=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@@H](C(=O)N[C@H]1CN(c2ccccc2N(C1=O)Cc3c4ccccc4ccc3OC)C(=O)c5ccc(cc5)N)NC

IUPAC InChI

InChI=1S/C32H33N5O4/c1-20(34-2)30(38)35-26-19-37(31(39)22-12-15-23(33)16-13-22)28-11-7-6-10-27(28)36(32(26)40)18-25-24-9-5-4-8-21(24)14-17-29(25)41-3/h4-17,20,26,34H,18-19,33H2,1-3H3,(H,35,38)/t20-,26-/m0/s1

IUPAC InChI key

BXNIMYHZUMCTGM-FNZWTVRRSA-N
1RH

wwPDB Information

Atom count

74 (41 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-05-08

Last modified at

2013-11-22

Status

Released

Obsoleted

Not Assigned



1RH : Atoms of Molecule

Total Number of Atoms: 74
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C28 C C28 N N N 0 -0.696 -3.453 1.905
2 O27 O O27 N N N 0 -0.522 -2.748 0.674
3 C26 C C26 N Y N 0 0.754 -2.542 0.256
4 C25 C C25 N Y N 0 1.818 -3.023 1.025
5 C24 C C24 N Y N 0 3.106 -2.833 0.633
6 C23 C C23 N Y N 0 3.377 -2.145 -0.563
7 C37 C C37 N Y N 0 4.695 -1.932 -0.998
8 C38 C C38 N Y N 0 4.921 -1.262 -2.161
9 C39 C C39 N Y N 0 3.862 -0.782 -2.93
10 C40 C C40 N Y N 0 2.572 -0.97 -2.54
11 C22 C C22 N Y N 0 2.3 -1.657 -1.345
12 C21 C C21 N Y N 0 0.981 -1.874 -0.914
13 C20 C C20 N N N 0 -0.178 -1.368 -1.734
14 N11 N N11 N N N 0 -0.771 -0.203 -1.073
15 C9 C C9 N N N 0 -1.87 -0.355 -0.303
16 O10 O O10 N N N 0 -2.309 -1.466 -0.093
17 C7 C C7 S N N 0 -2.552 0.845 0.298
18 C15 C C15 N N N 0 -1.743 1.372 1.484
19 N6 N N6 N N N 0 -3.891 0.465 0.755
20 C5 C C5 N N N 0 -4.922 0.457 -0.113
21 O8 O O8 N N N 0 -4.742 0.765 -1.272
22 C3 C C3 S N N 0 -6.3 0.065 0.357
23 C4 C C4 N N N 0 -6.265 -1.364 0.903
24 N2 N N2 N N N 0 -7.24 0.137 -0.769
25 C1 C C1 N N N 0 -8.614 0.352 -0.296
26 C12 C C12 N Y N 0 -0.193 1.061 -1.241
27 C16 C C16 N Y N 0 0.133 1.531 -2.502
28 C18 C C18 N Y N 0 0.729 2.772 -2.64
29 C17 C C17 N Y N 0 1.0 3.543 -1.525
30 C19 C C19 N Y N 0 0.671 3.084 -0.263
31 C13 C C13 N Y N 0 0.066 1.847 -0.116
32 N14 N N14 N N N 0 -0.319 1.393 1.144
33 C29 C C29 N N N 0 0.606 0.981 2.034
34 O30 O O30 N N N 0 0.257 0.468 3.079
35 C31 C C31 N Y N 0 2.041 1.152 1.739
36 C32 C C32 N Y N 0 2.471 1.307 0.418
37 C33 C C33 N Y N 0 3.81 1.467 0.146
38 C34 C C34 N Y N 0 4.737 1.474 1.186
39 N41 N N41 N N N 0 6.09 1.635 0.908
40 C35 C C35 N Y N 0 4.312 1.321 2.502
41 C36 C C36 N Y N 0 2.973 1.166 2.781
42 H1 H H1 N N N 0 -0.252 -4.445 1.821
43 H2 H H2 N N N 0 -0.209 -2.903 2.71
44 H3 H H3 N N N 0 -1.76 -3.548 2.122
45 H7 H H7 N N N 0 5.936 -1.099 -2.493
46 H4 H H4 N N N 0 1.614 -3.552 1.944
47 H5 H H5 N N N 0 3.918 -3.209 1.238
48 H6 H H6 N N N 0 5.526 -2.297 -0.413
49 H8 H H8 N N N 0 4.069 -0.253 -3.849
50 H9 H H9 N N N 0 1.761 -0.592 -3.146
51 H10 H H10 N N N 0 0.176 -1.083 -2.725
52 H11 H H11 N N N 0 -0.928 -2.154 -1.827
53 H12 H H12 N N N 0 -2.639 1.627 -0.456
54 H13 H H13 N N N 0 -2.072 2.382 1.728
55 H14 H H14 N N N 0 -1.899 0.723 2.346
56 H15 H H15 N N N 0 -4.036 0.218 1.682
57 H16 H H16 N N N 0 -6.623 0.747 1.144
58 H17 H H17 N N N 0 -5.942 -2.046 0.116
59 H18 H H18 N N N 0 -5.568 -1.416 1.739
60 H19 H H19 N N N 0 -7.261 -1.647 1.243
61 H20 H H20 N N N 0 -7.181 -0.692 -1.343
62 H22 H H22 N N N 0 -8.664 1.288 0.261
63 H23 H H23 N N N 0 -9.289 0.401 -1.15
64 H24 H H24 N N N 0 -8.908 -0.473 0.353
65 H25 H H25 N N N 0 -0.078 0.931 -3.374
66 H26 H H26 N N N 0 0.983 3.14 -3.624
67 H27 H H27 N N N 0 1.472 4.508 -1.641
68 H28 H H28 N N N 0 0.886 3.688 0.606
69 H29 H H29 N N N 0 1.753 1.3 -0.389
70 H30 H H30 N N N 0 4.143 1.586 -0.874
71 H31 H H31 N N N 0 6.387 1.743 -0.009
72 H32 H H32 N N N 0 6.736 1.641 1.631
73 H33 H H33 N N N 0 5.033 1.327 3.306
74 H34 H H34 N N N 0 2.643 1.05 3.803



1RH : Chemical Bonds

Total Number of Bonds: 78
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 N2 C N sing 1.47 N N
2 N2 C3 N C sing 1.47 N N
3 O8 C5 O C doub 1.21 N N
4 C3 C5 C C sing 1.51 N N
5 C3 C4 C C sing 1.53 N N
6 C5 N6 C N sing 1.35 N N
7 C18 C17 C C doub 1.38 N Y
8 C18 C16 C C sing 1.38 N Y
9 C17 C19 C C sing 1.38 N Y
10 N6 C7 N C sing 1.46 N N
11 C16 C12 C C doub 1.38 N Y
12 C7 C15 C C sing 1.53 N N
13 C7 C9 C C sing 1.51 N N
14 C19 C13 C C doub 1.38 N Y
15 C12 C13 C C sing 1.4 N Y
16 C12 N11 C N sing 1.4 N N
17 C15 N14 C N sing 1.46 N N
18 C13 N14 C N sing 1.39 N N
19 C9 N11 C N sing 1.35 N N
20 C9 O10 C O doub 1.21 N N
21 N11 C20 N C sing 1.46 N N
22 N14 C29 N C sing 1.35 N N
23 O27 C28 O C sing 1.43 N N
24 O27 C26 O C sing 1.36 N N
25 C20 C21 C C sing 1.51 N N
26 C29 O30 C O doub 1.22 N N
27 C29 C31 C C sing 1.47 N N
28 C26 C21 C C doub 1.37 N Y
29 C26 C25 C C sing 1.4 N Y
30 C31 C32 C C doub 1.4 N Y
31 C31 C36 C C sing 1.4 N Y
32 C21 C22 C C sing 1.4 N Y
33 C32 C33 C C sing 1.38 N Y
34 C36 C35 C C doub 1.38 N Y
35 C25 C24 C C doub 1.36 N Y
36 C33 C34 C C doub 1.39 N Y
37 C22 C40 C C doub 1.4 N Y
38 C22 C23 C C sing 1.42 N Y
39 C35 C34 C C sing 1.39 N Y
40 C40 C39 C C sing 1.36 N Y
41 C34 N41 C N sing 1.39 N N
42 C24 C23 C C sing 1.41 N Y
43 C23 C37 C C doub 1.4 N Y
44 C39 C38 C C doub 1.39 N Y
45 C37 C38 C C sing 1.36 N Y
46 C28 H1 C H sing 1.09 N N
47 C28 H2 C H sing 1.09 N N
48 C28 H3 C H sing 1.09 N N
49 C25 H4 C H sing 1.08 N N
50 C24 H5 C H sing 1.08 N N
51 C37 H6 C H sing 1.08 N N
52 C38 H7 C H sing 1.08 N N
53 C39 H8 C H sing 1.08 N N
54 C40 H9 C H sing 1.08 N N
55 C20 H10 C H sing 1.09 N N
56 C20 H11 C H sing 1.09 N N
57 C7 H12 C H sing 1.09 N N
58 C15 H13 C H sing 1.09 N N
59 C15 H14 C H sing 1.09 N N
60 N6 H15 N H sing 0.97 N N
61 C3 H16 C H sing 1.09 N N
62 C4 H17 C H sing 1.09 N N
63 C4 H18 C H sing 1.09 N N
64 C4 H19 C H sing 1.09 N N
65 N2 H20 N H sing 1.01 N N
66 C1 H22 C H sing 1.09 N N
67 C1 H23 C H sing 1.09 N N
68 C1 H24 C H sing 1.09 N N
69 C16 H25 C H sing 1.08 N N
70 C18 H26 C H sing 1.08 N N
71 C17 H27 C H sing 1.08 N N
72 C19 H28 C H sing 1.08 N N
73 C32 H29 C H sing 1.08 N N
74 C33 H30 C H sing 1.08 N N
75 N41 H31 N H sing 0.97 N N
76 N41 H32 N H sing 0.97 N N
77 C35 H33 C H sing 1.08 N N
78 C36 H34 C H sing 1.08 N N



1RH : Used in PDB Entries

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