Chemical Components in the PDB

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RX3 : Summary

Code

RX3

One-letter code

X

Molecule name

N-({(1S,2R)-2-[(S)-[(1R)-1-{[(BENZYLOXY)CARBONYL]AMINO}-2-PHENYLETHYL](HYDROXY)PHOSPHORYL]CYCLOPENTYL}CARBONYL)-L-TRYPT OPHAN

Synonyms

RXPA380

Systematic names

ProgramVersionName
ACDLabs 10.04 N-({(1S,2R)-2-[(S)-[(1R)-1-{[(benzyloxy)carbonyl]amino}-2-phenylethyl](hydroxy)phosphoryl]cyclopentyl}carbonyl)-L-tryptophan
OpenEye OEToolkits 1.5.0 (2S)-2-[[(1S)-2-[hydroxy-(2-phenyl-1-phenylmethoxycarbonylamino-ethyl)phosphoryl]cyclopentyl]carbonylamino]-3-(1H-indol-3-yl)propanoic acid

Formula

C33 H36 N3 O7 P

Formal charge

0

Molecular weight

617.629 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(OCc1ccccc1)NC(Cc2ccccc2)P(=O)(O)C5CCCC5C(=O)NC(C(=O)O)Cc4c3ccccc3nc4
SMILES CACTVS 3.341 OC(=O)[CH](Cc1c[nH]c2ccccc12)NC(=O)[CH]3CCC[CH]3[P](O)(=O)[CH](Cc4ccccc4)NC(=O)OCc5ccccc5
SMILES OpenEye OEToolkits 1.5.0 c1ccc(cc1)CC(NC(=O)OCc2ccccc2)P(=O)(C3CCCC3C(=O)NC(Cc4c[nH]c5c4cccc5)C(=O)O)O
Canonical SMILES CACTVS 3.341 OC(=O)[C@H](Cc1c[nH]c2ccccc12)NC(=O)[C@@H]3CCC[C@H]3[P@@](O)(=O)[C@H](Cc4ccccc4)NC(=O)OCc5ccccc5
Canonical SMILES OpenEye OEToolkits 1.5.0 c1ccc(cc1)CC(NC(=O)OCc2ccccc2)[P@](=O)(C3CCC[C@H]3C(=O)N[C@@H](Cc4c[nH]c5c4cccc5)C(=O)O)O

IUPAC InChI

InChI=1S/C33H36N3O7P/c37-31(35-28(32(38)39)19-24-20-34-27-16-8-7-14-25(24)27)26-15-9-17-29(26)44(41,42)30(18-22-10-3-1-4-11-22)36-33(40)43-21-23-12-5-2-6-13-23/h1-8,10-14,16,20,26,28-30,34H,9,15,17-19,21H2,(H,35,37)(H,36,40)(H,38,39)(H,41,42)/t26-,28+,29-,30-/m1/s1

IUPAC InChI key

IMPJIKIXNAGRCR-RRFVUZEHSA-N

Has sub-components

PPH , IQ0
RX3

wwPDB Information

Atom count

80 (44 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-01-04

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



RX3 : Atoms of Molecule

Total Number of Atoms: 80
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -1.627 -2.295 -4.675
2 O2 O O2 N N N 0 -1.961 -3.43 -4.353
3 O1 O O1 N N N 0 -0.413 -1.965 -5.207
4 C2 C C2 N N N 0 0.505 -3.049 -5.386
5 C3 C C3 N Y N 0 1.779 -2.521 -5.975
6 C4 C C4 N Y N 0 2.8 -2.092 -5.135
7 C6 C C6 N Y N 0 3.985 -1.6 -5.683
8 C8 C C8 N Y N 0 4.141 -1.541 -7.068
9 C7 C C7 N Y N 0 3.112 -1.974 -7.905
10 C5 C C5 N Y N 0 1.927 -2.465 -7.356
11 O3 O O3 N N N 0 -3.496 1.303 -2.782
12 P1 P P1 R N N 0 -3.684 -0.167 -2.542
13 O4 O O4 N N N 0 -5.054 -0.533 -1.762
14 C9 C C9 N N N 0 -3.765 -1.164 -4.032
15 N1 N N1 N N N 0 -2.408 -1.163 -4.563
16 C10 C C10 N N N 0 -4.759 -0.618 -5.063
17 C11 C C11 N Y N 0 -4.808 -1.427 -6.336
18 C12 C C12 N Y N 0 -5.7 -2.483 -6.437
19 C14 C C14 N Y N 0 -5.744 -3.231 -7.614
20 C16 C C16 N Y N 0 -4.897 -2.913 -8.675
21 C15 C C15 N Y N 0 -4.004 -1.847 -8.559
22 C13 C C13 N Y N 0 -3.959 -1.099 -7.382
23 C19 C C19 N N N 0 -0.94 0.559 -0.112
24 O5 O O5 N N N 0 0.061 -0.025 0.287
25 C18 C C18 R N N 0 -2.253 -0.161 -0.143
26 C20 C C20 N N N 0 -2.311 -1.227 0.953
27 C21 C C21 N N N 0 -2.046 -2.541 0.234
28 C22 C C22 N N N 0 -2.741 -2.347 -1.1
29 C17 C C17 N N N 0 -2.418 -0.903 -1.478
30 N2 N N2 N N N 0 -1.004 1.866 -0.556
31 C23 C C23 S N N 0 0.145 2.741 -0.607
32 C24 C C24 N N N 0 0.368 3.433 0.729
33 O6 O O6 N N N 0 1.33 4.161 0.951
34 C25 C C25 N N N 0 -0.005 3.786 -1.721
35 C26 C C26 N Y N 0 0.289 3.23 -3.093
36 C27 C C27 N Y N 0 -0.636 2.668 -3.911
37 C28 C C28 N Y N 0 1.548 3.217 -3.714
38 N3 N N3 N Y N 0 0.021 2.293 -5.053
39 C29 C C29 N Y N 0 1.356 2.617 -4.96
40 C30 C C30 N Y N 0 2.842 3.649 -3.361
41 C31 C C31 N Y N 0 2.398 2.426 -5.875
42 C32 C C32 N Y N 0 3.894 3.465 -4.266
43 C33 C C33 N Y N 0 3.673 2.862 -5.503
44 OXT O OXT N N N 0 -0.585 3.193 1.661
45 H21 H 1H2 N N N 0 0.05 -3.798 -6.043
46 H22 H 2H2 N N N 0 0.693 -3.523 -4.416
47 H4 H H4 N N N 0 2.688 -2.134 -4.055
48 H6 H H6 N N N 0 4.786 -1.263 -5.031
49 H8 H H8 N N N 0 5.064 -1.159 -7.495
50 H7 H H7 N N N 0 3.234 -1.928 -8.983
51 H5 H H5 N N N 0 1.131 -2.8 -8.016
52 HO4 H HO4 N N N 0 -5.711 -1.113 -2.203
53 H9 H H9 N N N 0 -4.033 -2.189 -3.75
54 HN1 H HN1 N N N 0 -2.015 -0.278 -4.87
55 H101 H 1H10 N N N 0 -5.767 -0.598 -4.63
56 H102 H 2H10 N N N 0 -4.523 0.428 -5.294
57 H12 H H12 N N N 0 -6.364 -2.739 -5.616
58 H14 H H14 N N N 0 -6.439 -4.061 -7.704
59 H16 H H16 N N N 0 -4.931 -3.495 -9.591
60 H15 H H15 N N N 0 -3.344 -1.599 -9.385
61 H13 H H13 N N N 0 -3.261 -0.271 -7.301
62 H18 H H18 N N N 0 -3.032 0.593 0.01
63 H201 H 1H20 N N N 0 -3.318 -1.248 1.388
64 H202 H 2H20 N N N 0 -1.598 -1.061 1.767
65 H17 H H17 N N N 0 -1.482 -0.884 -2.051
66 H211 H 1H21 N N N 0 -0.969 -2.684 0.087
67 H212 H 2H21 N N N 0 -2.435 -3.402 0.786
68 H221 H 1H22 N N N 0 -2.394 -3.057 -1.857
69 H222 H 2H22 N N N 0 -3.824 -2.481 -0.991
70 HN2 H HN2 N N N 0 -1.902 2.229 -0.86
71 H23 H H23 N N N 0 1.013 2.095 -0.78
72 H251 H 1H25 N N N 0 -1.025 4.192 -1.729
73 H252 H 2H25 N N N 0 0.647 4.647 -1.521
74 H27 H H27 N N N 0 -1.697 2.491 -3.807
75 HN3 H HN3 N N N 0 -0.41 1.844 -5.849
76 H30 H H30 N N N 0 3.03 4.121 -2.401
77 H31 H H31 N N N 0 2.227 1.957 -6.838
78 H32 H H32 N N N 0 4.893 3.797 -4.0
79 H33 H H33 N N N 0 4.503 2.729 -6.191
80 HOXT H HOXT N N N 0 -0.445 3.643 2.52



RX3 : Chemical Bonds

Total Number of Bonds: 84
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OXT C24 O C sing 1.35 N N
2 OXT HOXT O H sing 0.98 N N
3 C24 O6 C O doub 1.23 N N
4 C24 C23 C C sing 1.52 N N
5 C23 C25 C C sing 1.53 N N
6 C23 N2 C N sing 1.45 N N
7 C23 H23 C H sing 1.1 N N
8 C25 C26 C C sing 1.51 N N
9 C25 H251 C H sing 1.1 N N
10 C25 H252 C H sing 1.1 N N
11 C26 C27 C C doub 1.36 N Y
12 C26 C28 C C sing 1.4 N Y
13 C28 C29 C C sing 1.4 N Y
14 C28 C30 C C doub 1.41 N Y
15 C30 C32 C C sing 1.4 N Y
16 C30 H30 C H sing 1.09 N N
17 C32 C33 C C doub 1.39 N Y
18 C32 H32 C H sing 1.09 N N
19 C33 C31 C C sing 1.4 N Y
20 C33 H33 C H sing 1.09 N N
21 C31 C29 C C doub 1.4 N Y
22 C31 H31 C H sing 1.08 N N
23 C29 N3 C N sing 1.38 N Y
24 N3 C27 N C sing 1.37 N Y
25 N3 HN3 N H sing 1.01 N N
26 C27 H27 C H sing 1.08 N N
27 N2 C19 N C sing 1.38 N N
28 N2 HN2 N H sing 1.02 N N
29 C19 O5 C O doub 1.23 N N
30 C19 C18 C C sing 1.5 N N
31 C18 C20 C C sing 1.53 N N
32 C18 C17 C C sing 1.54 N N
33 C18 H18 C H sing 1.09 N N
34 C20 C21 C C sing 1.52 N N
35 C20 H201 C H sing 1.1 N N
36 C20 H202 C H sing 1.09 N N
37 C21 C22 C C sing 1.52 N N
38 C21 H211 C H sing 1.1 N N
39 C21 H212 C H sing 1.09 N N
40 C22 C17 C C sing 1.53 N N
41 C22 H221 C H sing 1.09 N N
42 C22 H222 C H sing 1.1 N N
43 C17 P1 C P sing 1.81 N N
44 C17 H17 C H sing 1.1 N N
45 P1 O3 P O doub 1.5 N N
46 P1 O4 P O sing 1.62 N N
47 P1 C9 P C sing 1.79 N N
48 O4 HO4 O H sing 0.98 N N
49 C9 C10 C C sing 1.53 N N
50 C9 N1 C N sing 1.46 N N
51 C9 H9 C H sing 1.1 N N
52 C10 C11 C C sing 1.51 N N
53 C10 H101 C H sing 1.1 N N
54 C10 H102 C H sing 1.1 N N
55 C11 C12 C C doub 1.39 N Y
56 C11 C13 C C sing 1.39 N Y
57 C13 C15 C C doub 1.4 N Y
58 C13 H13 C H sing 1.09 N N
59 C15 C16 C C sing 1.4 N Y
60 C15 H15 C H sing 1.09 N N
61 C16 C14 C C doub 1.39 N Y
62 C16 H16 C H sing 1.09 N N
63 C14 C12 C C sing 1.4 N Y
64 C14 H14 C H sing 1.09 N N
65 C12 H12 C H sing 1.09 N N
66 N1 C1 N C sing 1.38 N N
67 N1 HN1 N H sing 1.02 N N
68 C1 O2 C O doub 1.23 N N
69 C1 O1 C O sing 1.37 N N
70 O1 C2 O C sing 1.43 N N
71 C2 C3 C C sing 1.5 N N
72 C2 H21 C H sing 1.1 N N
73 C2 H22 C H sing 1.1 N N
74 C3 C4 C C sing 1.39 N Y
75 C3 C5 C C doub 1.39 N Y
76 C4 C6 C C doub 1.4 N Y
77 C4 H4 C H sing 1.09 N N
78 C5 C7 C C sing 1.4 N Y
79 C5 H5 C H sing 1.09 N N
80 C7 C8 C C doub 1.4 N Y
81 C7 H7 C H sing 1.09 N N
82 C8 C6 C C sing 1.4 N Y
83 C8 H8 C H sing 1.09 N N
84 C6 H6 C H sing 1.09 N N



RX3 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
RX3 2oc2 Open in New Window Bound ligand 1 1
RX3 2x96 Open in New Window Bound ligand 1 1