Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

PP7 : Summary

Code

PP7

One-letter code

X

Molecule name

METHYL CYCLO[(2S)-2-[[(1R)-1-(N-(L-N-(3-METHYLBUTANOYL)VALYL-L-ASPARTYL)AMINO)-3-METHYLBUTYL]HYDROXYPHOSPHINYLOXY]-3-(3-AMINOMETHYL)PHENYLPROPANOATE

Systematic names

ProgramVersionName
ACDLabs 10.04 methyl (6S,9R,10R,12S)-10-hydroxy-6-{[N-(3-methylbutanoyl)-L-valyl]amino}-9-(2-methylpropyl)-4,7-dioxo-11-oxa-3,8-diaza-10-phosphabicyclo[12.3.1]octadeca-1(18),14,16-triene-12-carboxylate 10-oxide
OpenEye OEToolkits 1.5.0 methyl (3S,5R,6R,9S)-5-hydroxy-9-[[(2S)-3-methyl-2-(3-methylbutanoylamino)butanoyl]amino]-6-(2-methylpropyl)-5,8,11-trioxo-4-oxa-7,12-diaza-5$l^{5}-phosphabicyclo[12.3.1]octadeca-1(17),14(18),15-triene-3-carboxylate

Formula

C30 H47 N4 O9 P

Formal charge

0

Molecular weight

638.689 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(NC(C(=O)NC2C(=O)NC(CC(C)C)P(=O)(O)OC(C(=O)OC)Cc1cc(ccc1)CNC(=O)C2)C(C)C)CC(C)C
SMILES CACTVS 3.341 COC(=O)[CH]1Cc2cccc(CNC(=O)C[CH](NC(=O)[CH](NC(=O)CC(C)C)C(C)C)C(=O)N[CH](CC(C)C)[P](O)(=O)O1)c2
SMILES OpenEye OEToolkits 1.5.0 CC(C)CC1NC(=O)C(CC(=O)NCc2cccc(c2)CC(OP1(=O)O)C(=O)OC)NC(=O)C(C(C)C)NC(=O)CC(C)C
Canonical SMILES CACTVS 3.341 COC(=O)[C@@H]1Cc2cccc(CNC(=O)C[C@H](NC(=O)[C@@H](NC(=O)CC(C)C)C(C)C)C(=O)N[C@@H](CC(C)C)[P@](O)(=O)O1)c2
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(C)C[C@@H]1NC(=O)[C@H](CC(=O)NCc2cccc(c2)C[C@H](O[P@]1(=O)O)C(=O)OC)NC(=O)[C@H](C(C)C)NC(=O)CC(C)C

IUPAC InChI

InChI=1S/C30H47N4O9P/c1-17(2)11-25(36)33-27(19(5)6)29(38)32-22-15-24(35)31-16-21-10-8-9-20(13-21)14-23(30(39)42-7)43-44(40,41)26(12-18(3)4)34-28(22)37/h8-10,13,17-19,22-23,26-27H,11-12,14-16H2,1-7H3,(H,31,35)(H,32,38)(H,33,36)(H,34,37)(H,40,41)/t22-,23-,26+,27-/m0/s1

IUPAC InChI key

BOYAGOIPWLIWCX-IDJLGEMNSA-N
PP7

wwPDB Information

Atom count

91 (44 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-08-23

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



PP7 : Atoms of Molecule

Total Number of Atoms: 91
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 NV2 N NV2 N N N 0 0.203 0.683 5.385
2 CV1 C CV1 N N N 0 0.938 1.985 7.356
3 CV6 C CV6 S N N 0 -0.014 -0.582 4.682
4 CV2 C CV2 N N N 0 1.52 1.704 8.743
5 CV7 C CV7 N N N 0 -1.424 -1.096 4.982
6 CV3 C CV3 N N N 0 1.749 3.027 9.478
7 CV8 C CV8 N N N 0 -2.454 -0.104 4.441
8 CV4 C CV4 N N N 0 0.543 0.84 9.541
9 CV9 C CV9 N N N 0 -1.624 -2.457 4.312
10 CV5 C CV5 N N N 0 0.714 0.682 6.633
11 CR C CR N N N 0 0.135 -0.366 3.198
12 OV1 O OV1 N N N 0 0.992 -0.367 7.173
13 OV2 O OV2 N N N 0 -0.093 0.724 2.719
14 N1 N N1 N N N 0 0.524 -1.383 2.404
15 C1 C C1 S N N 0 0.777 -1.146 0.981
16 C2 C C2 N N N 0 1.846 -2.121 0.484
17 C4 C C4 N N N 0 2.937 -1.355 -0.219
18 O2 O O2 N N N 0 3.46 -0.396 0.307
19 N2 N N2 N N N 0 3.325 -1.767 -1.467
20 CB C CB N N N 0 4.418 -0.957 -2.063
21 C3 C C3 N N N 0 -0.495 -1.359 0.202
22 O1 O O1 N N N 0 -1.131 -2.384 0.326
23 NL N NL N N N 0 -0.919 -0.378 -0.645
24 CAL C CAL R N N 0 -2.167 -0.659 -1.387
25 CBL C CBL N N N 0 -3.363 -0.116 -0.603
26 CGL C CGL N N N 0 -4.661 -0.535 -1.298
27 CL1 C CL1 N N N 0 -4.783 -2.06 -1.274
28 CL2 C CL2 N N N 0 -5.853 0.083 -0.566
29 P P P R N N 0 -2.079 0.154 -3.016
30 O3 O O3 N N N 0 -1.621 1.686 -2.825
31 O4 O O4 N N N 0 -3.411 0.114 -3.66
32 O5 O O5 N N N 0 -1.011 -0.612 -3.943
33 C5 C C5 S N N 0 -0.035 0.353 -4.338
34 C6 C C6 N N N 0 0.823 -0.219 -5.466
35 C7 C C7 N N N 0 -0.766 3.985 -5.237
36 CE2 C CE2 N Y N 0 2.275 -0.166 -5.069
37 CZ C CZ N Y N 0 3.222 0.286 -5.97
38 CD2 C CD2 N Y N 0 2.662 -0.568 -3.805
39 CE1 C CE1 N Y N 0 4.554 0.334 -5.607
40 CD1 C CD1 N Y N 0 4.941 -0.068 -4.342
41 CG C CG N Y N 0 3.995 -0.52 -3.441
42 CT C CT N N N 0 -0.73 1.601 -4.82
43 OT1 O OT1 N N N 0 -0.097 2.783 -4.772
44 OT2 O OT2 N N N 0 -1.858 1.536 -5.249
45 HV2 H HV2 N N N 0 -0.018 1.523 4.953
46 HV11 H 1HV1 N N N 0 1.635 2.601 6.788
47 HV12 H 2HV1 N N N 0 -0.01 2.511 7.46
48 HV6 H HV6 N N N 0 0.718 -1.316 5.018
49 HCV2 H HCV2 N N N 0 2.469 1.178 8.639
50 HCV7 H HCV7 N N N 0 -1.551 -1.2 6.06
51 HV31 H 1HV3 N N N 0 2.163 2.827 10.465
52 HV32 H 2HV3 N N N 0 2.445 3.643 8.909
53 HV33 H 3HV3 N N N 0 0.8 3.553 9.581
54 HV81 H 1HV8 N N N 0 -3.458 -0.469 4.655
55 HV82 H 2HV8 N N N 0 -2.311 0.865 4.918
56 HV83 H 3HV8 N N N 0 -2.327 0.0 3.363
57 HV41 H 1HV4 N N N 0 -0.405 1.366 9.645
58 HV43 H 3HV4 N N N 0 0.38 -0.102 9.018
59 HV42 H 2HV4 N N N 0 0.957 0.64 10.529
60 HV91 H 1HV9 N N N 0 -1.438 -2.365 3.242
61 HV92 H 2HV9 N N N 0 -0.93 -3.179 4.741
62 HV93 H 3HV9 N N N 0 -2.648 -2.795 4.475
63 H1 H H1 N N N 0 0.636 -2.272 2.776
64 H1A H H1A N N N 0 1.123 -0.122 0.839
65 HC21 H 1HC2 N N N 0 1.396 -2.831 -0.209
66 HC22 H 2HC2 N N N 0 2.269 -2.659 1.332
67 H2 H H2 N N N 0 2.921 -2.523 -1.922
68 HCB1 H 1HCB N N N 0 5.324 -1.559 -2.132
69 HCB2 H 2HCB N N N 0 4.604 -0.081 -1.442
70 HL H HL N N N 0 -0.432 0.453 -0.754
71 HAL H HAL N N N 0 -2.277 -1.735 -1.522
72 HL11 H 1HL1 N N N 0 -5.707 -2.358 -1.769
73 HBL1 H 1HBL N N N 0 -3.347 -0.519 0.409
74 HBL2 H 2HBL N N N 0 -3.308 0.971 -0.562
75 HGL H HGL N N N 0 -4.648 -0.187 -2.331
76 HL13 H 3HL1 N N N 0 -3.933 -2.5 -1.795
77 HL12 H 2HL1 N N N 0 -4.795 -2.407 -0.241
78 HL21 H 1HL2 N N N 0 -5.817 -0.194 0.487
79 HL23 H 3HL2 N N N 0 -5.813 1.168 -0.657
80 HL22 H 2HL2 N N N 0 -6.78 -0.284 -1.006
81 HO3 H HO3 N N N 0 -2.243 2.088 -2.203
82 HC5 H HC5 N N N 0 0.599 0.598 -3.486
83 HC61 H 1HC6 N N N 0 0.535 -1.254 -5.652
84 HC62 H 2HC6 N N N 0 0.672 0.367 -6.372
85 H7A H H7A N N N 0 -0.1 4.84 -5.121
86 H7B H H7B N N N 0 -1.031 3.87 -6.288
87 H7C H H7C N N N 0 -1.671 4.147 -4.65
88 HE1 H HE1 N N N 0 5.294 0.687 -6.311
89 HZ H HZ N N N 0 2.92 0.6 -6.958
90 HD2 H HD2 N N N 0 1.923 -0.922 -3.101
91 HD1 H HD1 N N N 0 5.982 -0.03 -4.058



PP7 : Chemical Bonds

Total Number of Bonds: 92
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 NV2 CV6 N C sing 1.46 N N
2 NV2 CV5 N C sing 1.35 N N
3 NV2 HV2 N H sing 0.97 N N
4 CV1 CV2 C C sing 1.53 N N
5 CV1 CV5 C C sing 1.51 N N
6 CV1 HV11 C H sing 1.09 N N
7 CV1 HV12 C H sing 1.09 N N
8 CV6 CV7 C C sing 1.53 N N
9 CV6 CR C C sing 1.51 N N
10 CV6 HV6 C H sing 1.09 N N
11 CV2 CV3 C C sing 1.53 N N
12 CV2 CV4 C C sing 1.53 N N
13 CV2 HCV2 C H sing 1.09 N N
14 CV7 CV8 C C sing 1.53 N N
15 CV7 CV9 C C sing 1.53 N N
16 CV7 HCV7 C H sing 1.09 N N
17 CV3 HV31 C H sing 1.09 N N
18 CV3 HV32 C H sing 1.09 N N
19 CV3 HV33 C H sing 1.09 N N
20 CV8 HV81 C H sing 1.09 N N
21 CV8 HV82 C H sing 1.09 N N
22 CV8 HV83 C H sing 1.09 N N
23 CV4 HV41 C H sing 1.09 N N
24 CV4 HV43 C H sing 1.09 N N
25 CV4 HV42 C H sing 1.09 N N
26 CV9 HV91 C H sing 1.09 N N
27 CV9 HV92 C H sing 1.09 N N
28 CV9 HV93 C H sing 1.09 N N
29 CV5 OV1 C O doub 1.21 N N
30 CR OV2 C O doub 1.21 N N
31 CR N1 C N sing 1.35 N N
32 N1 C1 N C sing 1.46 N N
33 N1 H1 N H sing 0.97 N N
34 C1 C2 C C sing 1.53 N N
35 C1 C3 C C sing 1.51 N N
36 C1 H1A C H sing 1.09 N N
37 C2 C4 C C sing 1.51 N N
38 C2 HC21 C H sing 1.09 N N
39 C2 HC22 C H sing 1.09 N N
40 C4 O2 C O doub 1.21 N N
41 C4 N2 C N sing 1.37 N N
42 N2 CB N C sing 1.49 N N
43 N2 H2 N H sing 0.97 N N
44 CB CG C C sing 1.51 N N
45 CB HCB1 C H sing 1.09 N N
46 CB HCB2 C H sing 1.09 N N
47 C3 O1 C O doub 1.21 N N
48 C3 NL C N sing 1.36 N N
49 NL CAL N C sing 1.48 N N
50 NL HL N H sing 0.97 N N
51 CAL CBL C C sing 1.53 N N
52 CAL P C P sing 1.82 N N
53 CAL HAL C H sing 1.09 N N
54 CBL CGL C C sing 1.53 N N
55 CBL HBL1 C H sing 1.09 N N
56 CBL HBL2 C H sing 1.09 N N
57 CGL CL1 C C sing 1.53 N N
58 CGL CL2 C C sing 1.53 N N
59 CGL HGL C H sing 1.09 N N
60 CL1 HL11 C H sing 1.09 N N
61 CL1 HL13 C H sing 1.09 N N
62 CL1 HL12 C H sing 1.09 N N
63 CL2 HL21 C H sing 1.09 N N
64 CL2 HL23 C H sing 1.09 N N
65 CL2 HL22 C H sing 1.09 N N
66 P O3 P O sing 1.61 N N
67 P O4 P O doub 1.48 N N
68 P O5 P O sing 1.61 N N
69 O3 HO3 O H sing 0.97 N N
70 O5 C5 O C sing 1.43 N N
71 C5 C6 C C sing 1.53 N N
72 C5 CT C C sing 1.51 N N
73 C5 HC5 C H sing 1.09 N N
74 C6 CE2 C C sing 1.51 N N
75 C6 HC61 C H sing 1.09 N N
76 C6 HC62 C H sing 1.09 N N
77 C7 OT1 C O sing 1.45 N N
78 C7 H7A C H sing 1.09 N N
79 C7 H7B C H sing 1.09 N N
80 C7 H7C C H sing 1.09 N N
81 CE2 CZ C C doub 1.38 N Y
82 CE2 CD2 C C sing 1.38 N Y
83 CZ CE1 C C sing 1.38 N Y
84 CZ HZ C H sing 1.08 N N
85 CD2 CG C C doub 1.38 N Y
86 CD2 HD2 C H sing 1.08 N N
87 CE1 CD1 C C doub 1.38 N Y
88 CE1 HE1 C H sing 1.08 N N
89 CD1 CG C C sing 1.38 N Y
90 CD1 HD1 C H sing 1.08 N N
91 CT OT1 C O sing 1.34 N N
92 CT OT2 C O doub 1.21 N N



PP7 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
PP7 1bxo Open in New Window Bound ligand 1 1