Chemical Components in the PDB

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4VJ : Summary

Code

4VJ

One-letter code

X

Molecule name

2-[(1S)-1-(3-chlorophenyl)-2-hydroxyethyl]-8-(2-{[(1S,3R)-3-hydroxycyclopentyl]amino}pyrimidin-4-yl)-2,3,4,5-tetrahydro-1H-pyrrolo[1,2-a][1,4]diazepin-1-one

Systematic names

ProgramVersionName
ACDLabs 12.01 2-[(1S)-1-(3-chlorophenyl)-2-hydroxyethyl]-8-(2-{[(1S,3R)-3-hydroxycyclopentyl]amino}pyrimidin-4-yl)-2,3,4,5-tetrahydro-1H-pyrrolo[1,2-a][1,4]diazepin-1-one
OpenEye OEToolkits 1.9.2 2-[(1S)-1-(3-chlorophenyl)-2-oxidanyl-ethyl]-8-[2-[[(1S,3R)-3-oxidanylcyclopentyl]amino]pyrimidin-4-yl]-4,5-dihydro-3H-pyrrolo[1,2-a][1,4]diazepin-1-one

Formula

C25 H28 Cl N5 O3

Formal charge

0

Molecular weight

481.975 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C4N(CCCn3cc(c2nc(NC1CCC(C1)O)ncc2)cc34)C(CO)c5cc(ccc5)Cl
SMILES CACTVS 3.385 OC[CH](N1CCCn2cc(cc2C1=O)c3ccnc(N[CH]4CC[CH](O)C4)n3)c5cccc(Cl)c5
SMILES OpenEye OEToolkits 1.9.2 c1cc(cc(c1)Cl)C(CO)N2CCCn3cc(cc3C2=O)c4ccnc(n4)NC5CCC(C5)O
Canonical SMILES CACTVS 3.385 OC[C@@H](N1CCCn2cc(cc2C1=O)c3ccnc(N[C@H]4CC[C@@H](O)C4)n3)c5cccc(Cl)c5
Canonical SMILES OpenEye OEToolkits 1.9.2 c1cc(cc(c1)Cl)[C@@H](CO)N2CCCn3cc(cc3C2=O)c4ccnc(n4)N[C@H]5CC[C@H](C5)O

IUPAC InChI

InChI=1S/C25H28ClN5O3/c26-18-4-1-3-16(11-18)23(15-32)31-10-2-9-30-14-17(12-22(30)24(31)34)21-7-8-27-25(29-21)28-19-5-6-20(33)13-19/h1,3-4,7-8,11-12,14,19-20,23,32-33H,2,5-6,9-10,13,15H2,(H,27,28,29)/t19-,20+,23+/m0/s1

IUPAC InChI key

ZQJZOIMPHMQLOK-MIZPHKNDSA-N
4VJ

wwPDB Information

Atom count

62 (34 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-06-05

Last modified at

2015-09-04

Status

Released

Obsoleted

Not Assigned



4VJ : Atoms of Molecule

Total Number of Atoms: 62
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2 O O1 N N N 0 -3.001 1.388 1.407
2 C11 C C1 N Y N 0 1.165 0.401 0.594
3 C12 C C2 N Y N 0 0.711 -0.502 -0.346
4 C13 C C3 N Y N 0 2.57 0.82 0.803
5 C14 C C4 N Y N 0 2.894 1.744 1.802
6 C15 C C5 N Y N 0 4.219 2.105 1.96
7 C16 C C6 N Y N 0 4.801 0.696 0.23
8 C17 C C7 N N N 0 -1.53 -1.461 -0.995
9 C18 C C8 N N N 0 -2.037 -2.618 -0.125
10 C19 C C9 N N N 0 -2.384 -2.101 1.27
11 C20 C C10 S N N 0 -4.595 -0.867 1.322
12 C21 C C11 N Y N 0 -5.161 -0.34 0.029
13 C22 C C12 N Y N 0 -6.13 0.646 0.049
14 C23 C C13 N Y N 0 -6.649 1.13 -1.138
15 C24 C C14 N Y N 0 -6.198 0.626 -2.346
16 C25 C C15 N Y N 0 -5.23 -0.359 -2.365
17 C26 C C16 N Y N 0 -4.707 -0.838 -1.178
18 C27 C C17 N N N 0 -5.083 -2.3 1.546
19 C28 C C18 S N N 0 7.186 0.56 -0.386
20 C29 C C19 N N N 0 7.982 0.327 -1.687
21 C30 C C20 R N N 0 9.373 -0.151 -1.202
22 CL1 CL CL1 N N N 0 -7.866 2.367 -1.113
23 N3 N N1 N Y N 0 5.136 1.569 1.168
24 N5 N N2 N N N 0 -3.132 -0.854 1.257
25 C31 C C21 N N N 0 9.022 -1.045 0.014
26 C8 C C22 N Y N 0 -1.039 0.223 0.796
27 O34 O O2 N N N 0 10.03 -0.912 -2.217
28 C32 C C23 N N N 0 7.848 -0.312 0.695
29 C10 C C24 N Y N 0 0.038 0.855 1.316
30 C9 C C25 N N N 0 -2.46 0.321 1.183
31 N1 N N3 N Y N 0 -0.621 -0.616 -0.219
32 N7 N N4 N N N 0 5.791 0.155 -0.572
33 O6 O O3 N N N 0 -4.748 -3.1 0.41
34 N4 N N5 N Y N 0 3.545 0.319 0.048
35 H1 H H1 N N N 0 1.324 -1.028 -1.063
36 H2 H H2 N N N 0 2.127 2.167 2.434
37 H3 H H3 N N N 0 4.504 2.816 2.721
38 H4 H H4 N N N 0 -1.002 -1.862 -1.86
39 H5 H H5 N N N 0 -2.377 -0.864 -1.335
40 H6 H H6 N N N 0 -2.927 -3.052 -0.582
41 H7 H H7 N N N 0 -1.262 -3.379 -0.047
42 H8 H H8 N N N 0 -2.976 -2.858 1.786
43 H9 H H9 N N N 0 -1.458 -1.945 1.825
44 H10 H H10 N N N 0 -4.928 -0.238 2.148
45 H11 H H11 N N N 0 -6.482 1.038 0.992
46 H12 H H12 N N N 0 -6.606 1.0 -3.273
47 H13 H H13 N N N 0 -4.878 -0.752 -3.307
48 H14 H H14 N N N 0 -3.95 -1.608 -1.193
49 H15 H H15 N N N 0 -4.604 -2.713 2.434
50 H16 H H16 N N N 0 -6.164 -2.299 1.683
51 H17 H H17 N N N 0 7.236 1.61 -0.101
52 H18 H H18 N N N 0 7.504 -0.443 -2.294
53 H19 H H19 N N N 0 8.073 1.256 -2.25
54 H20 H H20 N N N 0 9.988 0.696 -0.898
55 H21 H H21 N N N 0 8.713 -2.036 -0.318
56 H22 H H22 N N N 0 9.873 -1.118 0.691
57 H23 H H23 N N N 0 10.905 -1.235 -1.963
58 H24 H H24 N N N 0 8.219 0.315 1.505
59 H25 H H25 N N N 0 7.13 -1.036 1.082
60 H26 H H26 N N N 0 0.037 1.569 2.127
61 H27 H H27 N N N 0 5.56 -0.491 -1.258
62 H28 H H28 N N N 0 -5.027 -4.023 0.482



4VJ : Chemical Bonds

Total Number of Bonds: 66
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C24 C25 C C doub 1.38 N Y
2 C24 C23 C C sing 1.38 N Y
3 C15 C14 C C doub 1.38 N Y
4 C15 N3 C N sing 1.32 N Y
5 C25 C26 C C sing 1.38 N Y
6 C14 C13 C C sing 1.4 N Y
7 CL1 C23 CL C sing 1.74 N N
8 C23 C22 C C doub 1.38 N Y
9 N3 C16 N C doub 1.32 N Y
10 C26 C21 C C doub 1.38 N Y
11 C10 C11 C C sing 1.41 N Y
12 C10 C8 C C doub 1.35 N Y
13 O2 C9 O C doub 1.22 N N
14 C13 C11 C C sing 1.48 N N
15 C13 N4 C N doub 1.33 N Y
16 C22 C21 C C sing 1.38 N Y
17 C16 N4 C N sing 1.32 N Y
18 C16 N7 C N sing 1.38 N N
19 C21 C20 C C sing 1.51 N N
20 C11 C12 C C doub 1.38 N Y
21 C9 C8 C C sing 1.48 N N
22 C9 N5 C N sing 1.36 N N
23 C8 N1 C N sing 1.38 N Y
24 N7 C28 N C sing 1.46 N N
25 N5 C20 N C sing 1.46 N N
26 N5 C19 N C sing 1.45 N N
27 C20 C27 C C sing 1.53 N N
28 C12 N1 C N sing 1.34 N Y
29 N1 C17 N C sing 1.46 N N
30 C28 C32 C C sing 1.54 N N
31 C28 C29 C C sing 1.54 N N
32 C32 C31 C C sing 1.54 N N
33 C19 C18 C C sing 1.53 N N
34 C27 O6 C O sing 1.43 N N
35 C17 C18 C C sing 1.53 N N
36 C29 C30 C C sing 1.55 N N
37 C31 C30 C C sing 1.55 N N
38 C30 O34 C O sing 1.43 N N
39 C12 H1 C H sing 1.08 N N
40 C14 H2 C H sing 1.08 N N
41 C15 H3 C H sing 1.08 N N
42 C17 H4 C H sing 1.09 N N
43 C17 H5 C H sing 1.09 N N
44 C18 H6 C H sing 1.09 N N
45 C18 H7 C H sing 1.09 N N
46 C19 H8 C H sing 1.09 N N
47 C19 H9 C H sing 1.09 N N
48 C20 H10 C H sing 1.09 N N
49 C22 H11 C H sing 1.08 N N
50 C24 H12 C H sing 1.08 N N
51 C25 H13 C H sing 1.08 N N
52 C26 H14 C H sing 1.08 N N
53 C27 H15 C H sing 1.09 N N
54 C27 H16 C H sing 1.09 N N
55 C28 H17 C H sing 1.09 N N
56 C29 H18 C H sing 1.09 N N
57 C29 H19 C H sing 1.09 N N
58 C30 H20 C H sing 1.09 N N
59 C31 H21 C H sing 1.09 N N
60 C31 H22 C H sing 1.09 N N
61 O34 H23 O H sing 0.97 N N
62 C32 H24 C H sing 1.09 N N
63 C32 H25 C H sing 1.09 N N
64 C10 H26 C H sing 1.08 N N
65 N7 H27 N H sing 0.97 N N
66 O6 H28 O H sing 0.97 N N



4VJ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
4VJ 5bvf Open in New Window Bound ligand 1 1