Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

YVN : Summary

Code

YVN

One-letter code

X

Molecule name

N-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-L-valyl-L-aspartamide

Systematic names

ProgramVersionName
ACDLabs 10.04 N-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-L-valyl-L-aspartamide
OpenEye OEToolkits 1.5.0 [4-[(1S,2R,3R)-2-[[(2S)-1-[[(2S)-1,4-diamino-1,4-dioxo-butan-2-yl]amino]-3-methyl-1-oxo-butan-2-yl]carbamoyl]-3-(methylcarbamoyl)cyclopropyl]phenyl] dihydrogen phosphate

Formula

C21 H30 N5 O9 P

Formal charge

0

Molecular weight

527.465 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(N)CC(C(=O)N)NC(=O)C(NC(=O)C2C(C(=O)NC)C2c1ccc(OP(=O)(O)O)cc1)C(C)C
SMILES CACTVS 3.341 CNC(=O)[CH]1[CH]([CH]1c2ccc(O[P](O)(O)=O)cc2)C(=O)N[CH](C(C)C)C(=O)N[CH](CC(N)=O)C(N)=O
SMILES OpenEye OEToolkits 1.5.0 CC(C)C(C(=O)NC(CC(=O)N)C(=O)N)NC(=O)C1C(C1C(=O)NC)c2ccc(cc2)OP(=O)(O)O
Canonical SMILES CACTVS 3.341 CNC(=O)[C@H]1[C@@H]([C@H]1c2ccc(O[P](O)(O)=O)cc2)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CC(N)=O)C(N)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC(C)[C@@H](C(=O)N[C@@H](CC(=O)N)C(=O)N)NC(=O)[C@@H]1[C@H]([C@H]1C(=O)NC)c2ccc(cc2)OP(=O)(O)O

IUPAC InChI

InChI=1S/C21H30N5O9P/c1-9(2)17(21(31)25-12(18(23)28)8-13(22)27)26-20(30)16-14(15(16)19(29)24-3)10-4-6-11(7-5-10)35-36(32,33)34/h4-7,9,12,14-17H,8H2,1-3H3,(H2,22,27)(H2,23,28)(H,24,29)(H,25,31)(H,26,30)(H2,32,33,34)/t12-,14-,15+,16+,17-/m0/s1

IUPAC InChI key

LVYNAUCEOQBVSW-RDDKANTKSA-N
YVN

wwPDB Information

Atom count

66 (36 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-08-01

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



YVN : Atoms of Molecule

Total Number of Atoms: 66
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OBH O OBH N N N 0 7.426 1.758 -1.189
2 PBF P PBF N N N 0 7.242 2.106 0.237
3 OBI O OBI N N N 0 8.668 2.47 0.889
4 OBG O OBG N N N 0 6.258 3.374 0.357
5 OBE O OBE N N N 0 6.599 0.852 1.017
6 CBD C CBD N Y N 0 5.44 0.398 0.473
7 CBC C CBC N Y N 0 4.225 0.923 0.888
8 CBB C CBB N Y N 0 3.047 0.459 0.334
9 CBJ C CBJ N Y N 0 5.47 -0.587 -0.503
10 CBK C CBK N Y N 0 4.29 -1.047 -1.055
11 CBA C CBA N Y N 0 3.079 -0.527 -0.635
12 CAZ C CAZ S N N 0 1.794 -1.031 -1.237
13 CAF C CAF R N N 0 1.249 -2.366 -0.726
14 CAC C CAC N N N 0 2.039 -3.076 0.343
15 OAD O OAD N N N 0 2.976 -2.52 0.875
16 NAB N NAB N N N 0 1.705 -4.33 0.707
17 CAA C CAA N N N 0 2.473 -5.02 1.746
18 CAG C CAG R N N 0 0.555 -1.058 -0.34
19 CAH C CAH N N N 0 -0.776 -0.761 -0.981
20 OAI O OAI N N N 0 -0.836 -0.512 -2.166
21 NAJ N NAJ N N N 0 -1.9 -0.771 -0.237
22 CAK C CAK S N N 0 -3.194 -0.482 -0.86
23 CAW C CAW N N N 0 -3.762 -1.764 -1.472
24 CAX C CAX N N N 0 -2.873 -2.213 -2.633
25 CAY C CAY N N N 0 -3.805 -2.862 -0.408
26 CAL C CAL N N N 0 -4.147 0.043 0.182
27 OAM O OAM N N N 0 -3.846 0.0 1.356
28 NAN N NAN N N N 0 -5.334 0.561 -0.19
29 CAO C CAO S N N 0 -6.218 1.161 0.812
30 CAT C CAT N N N 0 -7.053 0.084 1.455
31 OAV O OAV N N N 0 -6.923 -1.071 1.11
32 NAU N NAU N N N 0 -7.945 0.405 2.413
33 CAP C CAP N N N 0 -7.136 2.182 0.136
34 CAQ C CAQ N N N 0 -6.309 3.323 -0.401
35 OAS O OAS N N N 0 -5.105 3.319 -0.257
36 NAR N NAR N N N 0 -6.908 4.346 -1.041
37 HOBI H HOBI N N N 0 9.114 3.217 0.468
38 HOBG H HOBG N N N 0 6.091 3.658 1.267
39 HBC H HBC N N N 0 4.199 1.693 1.645
40 HBB H HBB N N N 0 2.101 0.868 0.657
41 HBJ H HBJ N N N 0 6.415 -0.994 -0.832
42 HBK H HBK N N N 0 4.312 -1.814 -1.815
43 HAZ H HAZ N N N 0 1.646 -0.798 -2.292
44 HAF H HAF N N N 0 0.743 -3.011 -1.443
45 HNAB H HNAB N N N 0 0.955 -4.775 0.282
46 HAA1 H HAA1 N N N 0 2.42 -4.453 2.675
47 HAA2 H HAA2 N N N 0 2.058 -6.016 1.904
48 HAA3 H HAA3 N N N 0 3.513 -5.106 1.432
49 HAG H HAG N N N 0 0.67 -0.711 0.687
50 HNAJ H HNAJ N N N 0 -1.852 -0.97 0.712
51 HAK H HAK N N N 0 -3.061 0.266 -1.641
52 HAW H HAW N N N 0 -4.771 -1.574 -1.839
53 HAX1 H HAX1 N N N 0 -1.891 -2.494 -2.252
54 HAX2 H HAX2 N N N 0 -3.329 -3.07 -3.129
55 HAX3 H HAX3 N N N 0 -2.766 -1.395 -3.346
56 HAY1 H HAY1 N N N 0 -4.438 -2.542 0.42
57 HAY2 H HAY2 N N N 0 -4.21 -3.775 -0.844
58 HAY3 H HAY3 N N N 0 -2.796 -3.051 -0.041
59 HNAN H HNAN N N N 0 -5.603 0.536 -1.122
60 HAO H HAO N N N 0 -5.619 1.66 1.573
61 HAU1 H HAU1 N N N 0 -8.05 1.329 2.688
62 HAU2 H HAU2 N N N 0 -8.483 -0.288 2.827
63 HAP1 H HAP1 N N N 0 -7.67 1.704 -0.685
64 HAP2 H HAP2 N N N 0 -7.852 2.564 0.863
65 HAR1 H HAR1 N N N 0 -7.871 4.35 -1.156
66 HAR2 H HAR2 N N N 0 -6.376 5.08 -1.386



YVN : Chemical Bonds

Total Number of Bonds: 67
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OBH PBF O P doub 1.48 N N
2 PBF OBI P O sing 1.61 N N
3 PBF OBE P O sing 1.61 N N
4 PBF OBG P O sing 1.61 N N
5 OBI HOBI O H sing 0.97 N N
6 OBG HOBG O H sing 0.97 N N
7 OBE CBD O C sing 1.36 N N
8 CBD CBJ C C doub 1.39 N Y
9 CBD CBC C C sing 1.39 N Y
10 CBC CBB C C doub 1.38 N Y
11 CBC HBC C H sing 1.08 N N
12 CBB CBA C C sing 1.38 N Y
13 CBB HBB C H sing 1.08 N N
14 CBJ CBK C C sing 1.38 N Y
15 CBJ HBJ C H sing 1.08 N N
16 CBK CBA C C doub 1.38 N Y
17 CBK HBK C H sing 1.08 N N
18 CBA CAZ C C sing 1.51 N N
19 CAZ CAG C C sing 1.53 N N
20 CAZ CAF C C sing 1.53 N N
21 CAZ HAZ C H sing 1.09 N N
22 CAF CAG C C sing 1.53 N N
23 CAF CAC C C sing 1.51 N N
24 CAF HAF C H sing 1.09 N N
25 CAC OAD C O doub 1.21 N N
26 CAC NAB C N sing 1.35 N N
27 NAB CAA N C sing 1.46 N N
28 NAB HNAB N H sing 0.97 N N
29 CAA HAA1 C H sing 1.09 N N
30 CAA HAA2 C H sing 1.09 N N
31 CAA HAA3 C H sing 1.09 N N
32 CAG CAH C C sing 1.51 N N
33 CAG HAG C H sing 1.09 N N
34 CAH NAJ C N sing 1.35 N N
35 CAH OAI C O doub 1.21 N N
36 NAJ CAK N C sing 1.46 N N
37 NAJ HNAJ N H sing 0.97 N N
38 CAK CAW C C sing 1.53 N N
39 CAK CAL C C sing 1.51 N N
40 CAK HAK C H sing 1.09 N N
41 CAW CAY C C sing 1.53 N N
42 CAW CAX C C sing 1.53 N N
43 CAW HAW C H sing 1.09 N N
44 CAX HAX1 C H sing 1.09 N N
45 CAX HAX2 C H sing 1.09 N N
46 CAX HAX3 C H sing 1.09 N N
47 CAY HAY1 C H sing 1.09 N N
48 CAY HAY2 C H sing 1.09 N N
49 CAY HAY3 C H sing 1.09 N N
50 CAL NAN C N sing 1.35 N N
51 CAL OAM C O doub 1.21 N N
52 NAN CAO N C sing 1.46 N N
53 NAN HNAN N H sing 0.97 N N
54 CAO CAP C C sing 1.53 N N
55 CAO CAT C C sing 1.51 N N
56 CAO HAO C H sing 1.09 N N
57 CAT NAU C N sing 1.35 N N
58 CAT OAV C O doub 1.21 N N
59 NAU HAU1 N H sing 0.97 N N
60 NAU HAU2 N H sing 0.97 N N
61 CAP CAQ C C sing 1.51 N N
62 CAP HAP1 C H sing 1.09 N N
63 CAP HAP2 C H sing 1.09 N N
64 CAQ NAR C N sing 1.35 N N
65 CAQ OAS C O doub 1.21 N N
66 NAR HAR1 N H sing 0.97 N N
67 NAR HAR2 N H sing 0.97 N N



YVN : Used in PDB Entries

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