Receptor
PDB id Resolution Class Description Source Keywords
2YNC 1.75 Å EC: 2.3.1.97 PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH YNC12-COA THIOESTER. PLASMODIUM VIVAX TRANSFERASE MYRISTOYLATION MALARIA
Ref.: VALIDATION OF N-MYRISTOYLTRANSFERASE AS AN ANTIMALA DRUG TARGET USING AN INTEGRATED CHEMICAL BIOLOGY AP NAT.CHEM. V. 6 112 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
YNC A:1000;
B:1000;
C:1000;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
973.858 C35 H58 N7 O17 P3 S CC(C)...
DMS A:999;
C:999;
B:999;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
78.133 C2 H6 O S CS(=O...
CL B:1412;
A:1500;
C:1412;
A:1413;
C:1500;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
35.453 Cl [Cl-]
MG A:1412;
C:1411;
B:1411;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
SO4 A:1411;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2YNC 1.75 Å EC: 2.3.1.97 PLASMODIUM VIVAX N-MYRISTOYLTRANSFERASE IN COMPLEX WITH YNC12-COA THIOESTER. PLASMODIUM VIVAX TRANSFERASE MYRISTOYLATION MALARIA
Ref.: VALIDATION OF N-MYRISTOYLTRANSFERASE AS AN ANTIMALA DRUG TARGET USING AN INTEGRATED CHEMICAL BIOLOGY AP NAT.CHEM. V. 6 112 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2YNC - YNC C35 H58 N7 O17 P3 S CC(C)(COP(....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 7 families.
1 2YNC - YNC C35 H58 N7 O17 P3 S CC(C)(COP(....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2YNC - YNC C35 H58 N7 O17 P3 S CC(C)(COP(....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YNC; Similar ligands found: 119
No: Ligand ECFP6 Tc MDL keys Tc
1 YNC 1 1
2 MFK 0.876812 0.945055
3 ST9 0.876812 0.945055
4 5F9 0.876812 0.945055
5 UCC 0.876812 0.945055
6 DCC 0.876812 0.945055
7 MYA 0.876812 0.945055
8 CO8 0.869565 0.945055
9 HXC 0.855072 0.945055
10 GRA 0.828571 0.966292
11 1HE 0.818841 0.945055
12 BCO 0.818841 0.966292
13 SCA 0.807143 0.966292
14 1VU 0.804348 0.955556
15 IVC 0.792857 0.977273
16 MLC 0.792857 0.966292
17 3HC 0.792857 0.977273
18 ACO 0.788321 0.955556
19 CAA 0.787234 0.977273
20 3KK 0.776978 0.966292
21 HGG 0.776224 0.966292
22 COS 0.773723 0.944444
23 CAO 0.773723 0.934066
24 OXK 0.771429 0.966292
25 FAQ 0.770833 0.966292
26 CO6 0.765957 0.966292
27 2MC 0.760563 0.945652
28 TGC 0.760274 0.955556
29 COK 0.758865 0.944444
30 HDC 0.758389 0.945055
31 FYN 0.751773 0.965909
32 IRC 0.751724 0.977273
33 CS8 0.751678 0.934783
34 MCA 0.75 0.955556
35 COO 0.75 0.988636
36 SOP 0.746479 0.944444
37 MC4 0.744828 0.935484
38 CMC 0.741259 0.944444
39 1GZ 0.739726 0.977528
40 BYC 0.739726 0.966292
41 COW 0.739726 0.955556
42 COA 0.73913 0.965909
43 0T1 0.73913 0.94382
44 DCA 0.737226 0.922222
45 30N 0.735714 0.885417
46 AMX 0.735714 0.954545
47 BCA 0.734694 0.955556
48 2NE 0.731544 0.945055
49 A1S 0.731034 0.944444
50 CMX 0.730496 0.94382
51 MRS 0.730263 0.945055
52 MRR 0.730263 0.945055
53 COF 0.727891 0.923913
54 3CP 0.727891 0.944444
55 ETB 0.724638 0.89011
56 CAJ 0.724138 0.923077
57 UOQ 0.723684 0.923913
58 NHM 0.723684 0.923913
59 NHW 0.723684 0.923913
60 0ET 0.721854 0.923913
61 2CP 0.721088 0.934066
62 8Z2 0.720779 0.956044
63 HAX 0.72028 0.923077
64 1CZ 0.72 0.955556
65 SCO 0.71831 0.94382
66 2KQ 0.716216 0.945055
67 FCX 0.713287 0.913043
68 FAM 0.713287 0.923077
69 SCD 0.712329 0.94382
70 4CA 0.711409 0.934066
71 MCD 0.710345 0.923077
72 CA6 0.710345 0.858586
73 WCA 0.705882 0.966667
74 NMX 0.705479 0.875
75 DAK 0.703226 0.956044
76 4KX 0.701299 0.956044
77 UCA 0.701219 0.945055
78 CIC 0.697368 0.944444
79 1CV 0.694805 0.966292
80 4CO 0.69281 0.934066
81 0FQ 0.69281 0.944444
82 01A 0.688312 0.904255
83 CCQ 0.686275 0.924731
84 CA8 0.682119 0.877551
85 1HA 0.68125 0.945055
86 YE1 0.68 0.933333
87 NHQ 0.679245 0.955056
88 COA MYR 0.677419 0.913043
89 COA PLM 0.677419 0.913043
90 PLM COA 0.677419 0.913043
91 HFQ 0.675159 0.923913
92 01K 0.666667 0.944444
93 S0N 0.664516 0.923077
94 CA3 0.654545 0.944444
95 COT 0.652439 0.944444
96 CA5 0.64497 0.904255
97 CO7 0.636364 0.988636
98 93P 0.631579 0.934066
99 93M 0.622857 0.934066
100 COD 0.60274 0.954545
101 JBT 0.590426 0.886598
102 5TW 0.589189 0.925532
103 4BN 0.589189 0.925532
104 HMG 0.582822 0.933333
105 OXT 0.578378 0.905263
106 BSJ 0.534392 0.913979
107 191 0.5 0.877551
108 PAP 0.496296 0.784091
109 SFC 0.47486 0.945055
110 RFC 0.47486 0.945055
111 PPS 0.47482 0.729167
112 ACE SER ASP ALY THR NH2 COA 0.472637 0.902174
113 0WD 0.453416 0.782609
114 A3P 0.451852 0.772727
115 PTJ 0.414474 0.842697
116 PUA 0.414201 0.813187
117 3AM 0.407407 0.761364
118 A22 0.402685 0.786517
119 NA7 0.401316 0.829545
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YNC; Ligand: YNC; Similar sites found: 192
This union binding pocket(no: 1) in the query (biounit: 2ync.bio2) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2AWN ADP 0.005292 0.46482 1.31234
2 4PPF FLC 0.001125 0.50311 1.42857
3 3PMA SCR 0.03303 0.4188 1.5444
4 2Q8H TF4 0.02058 0.41444 1.5625
5 5GK9 ACO 0.00005119 0.4879 1.81159
6 3D2M COA 0.00005892 0.47779 2.08333
7 5JPH COA 0.000598 0.46674 2.08333
8 5TSH ADP 0.005731 0.45904 2.08333
9 3BJC WAN 0.007691 0.4482 2.08333
10 3LN9 FLC 0.01344 0.45062 2.15827
11 1XP8 AGS 0.01884 0.42281 2.18579
12 2VZZ SCA 0.0001634 0.46046 2.29358
13 3SHZ 5CO 0.01758 0.42035 2.30548
14 4KJU 1RH 0.04544 0.40685 2.32558
15 1G6H ADP 0.01091 0.44628 2.33463
16 1M0W ANP 0.01074 0.42351 2.34375
17 2D2F ADP 0.009682 0.44208 2.4
18 3TK1 GDP 0.0381 0.41041 2.42424
19 4B5P ACO 0.00005634 0.48622 2.5
20 4H6U ACO 0.0003849 0.47116 2.5
21 5CX6 CDP 0.03994 0.41058 2.60417
22 2WH8 II2 0.02963 0.40504 2.60417
23 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 0.03552 0.41599 2.6087
24 1U0J ADP 0.01954 0.42197 2.62172
25 1RRC ADP 0.02063 0.42905 2.65781
26 3KC1 2T6 0.009155 0.41638 2.67062
27 4AVB ACO 0.00007034 0.49042 2.7027
28 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 0.02739 0.42029 2.72109
29 4WZ6 ATP 0.03572 0.41394 2.75862
30 1JGS SAL 0.04679 0.40321 2.89855
31 3COB ADP 0.04466 0.40907 2.98103
32 2ZW5 COA 0.0002384 0.47614 2.99003
33 1XMV ADP 0.01544 0.41939 3.08989
34 1BG2 ADP 0.01495 0.43351 3.125
35 1RTW MP5 0.04217 0.40799 3.18182
36 3EC1 GDP 0.02226 0.41135 3.25203
37 1GXU 2HP 0.0007534 0.48169 3.2967
38 4KFU ACP 0.01481 0.43579 3.30189
39 4R2I ANP 0.01656 0.43015 3.33333
40 1GOJ ADP 0.04019 0.40942 3.38028
41 4MRP GSH 0.01059 0.44563 3.38542
42 1YQT ADP 0.01639 0.43138 3.38542
43 1J78 OLA 0.03021 0.4219 3.38542
44 3A51 VDY 0.03085 0.40415 3.38542
45 1J78 VDY 0.04468 0.40281 3.38542
46 1XMY ROL 0.0457 0.40229 3.38542
47 4DOO DAO 0.01653 0.40759 3.41463
48 1R0X ATP 0.04332 0.40734 3.4965
49 2WPX ACO 0.00003441 0.53368 3.53982
50 2WPW ACO 0.00008235 0.52143 3.53982
51 5UC9 MYR 0.02231 0.42627 3.53982
52 3ITJ CIT 0.02557 0.42133 3.5503
53 3NX2 FER 0.02952 0.40842 3.57143
54 2ZPA ACO 0.000008182 0.53975 3.57675
55 5FPN KYD 0.005144 0.44967 3.64583
56 2X1L MET 0.01283 0.43795 3.64583
57 3RC3 ANP 0.0181 0.42374 3.64583
58 4AG5 ADP 0.0492 0.40611 3.64583
59 2YGM GLA NAG GAL FUC 0.0258 0.41556 3.67232
60 2ZR9 DTP 0.008147 0.43758 3.72493
61 1JI0 ATP 0.01467 0.43302 3.75
62 4NON GDP 0.04066 0.40141 3.84615
63 1TIQ COA 0.0002456 0.50401 3.88889
64 5VRH OLB 0.005149 0.46131 3.90625
65 2ZFN ACO 0.003643 0.41859 3.90625
66 3LRE ADP 0.02995 0.41753 3.94366
67 1OXV ANP 0.02356 0.41766 3.96601
68 2B4D COA 0.0004741 0.47129 4.09357
69 1SQ5 ADP 0.03316 0.40256 4.22078
70 4XPL ACO 0.006844 0.42567 4.29448
71 5TVI MYR 0.009355 0.47658 4.34783
72 2ALG DAO 0.03324 0.41637 4.34783
73 5CHR 4NC 0.02979 0.41914 4.37956
74 1WWZ ACO 0.00002255 0.49814 4.40252
75 3W5J GDP 0.03589 0.41466 4.41176
76 3B9Z CO2 0.01277 0.45049 4.42708
77 3AQT RCO 0.02987 0.4171 4.4898
78 2X7I CIT 0.008837 0.43577 4.54545
79 3KP6 SAL 0.01042 0.44314 4.63576
80 5V3Y 5V8 0.03238 0.40658 4.8951
81 5HGZ ACO 0.00001182 0.52286 4.93827
82 1M4I COA 0.00004899 0.45526 4.97238
83 1M4I PAP 0.00004899 0.45526 4.97238
84 1M4I KAN 0.00004899 0.45526 4.97238
85 5DXG EST 0.02733 0.40683 4.98084
86 2OG2 MLI 0.008258 0.42403 5.01393
87 2QA8 GEN 0.0316 0.40032 5.03876
88 3TE4 ACO 0.000003349 0.5566 5.11628
89 4TV1 36M 0.02409 0.42129 5.17928
90 3UU7 2OH 0.03073 0.41764 5.17928
91 3UUA 0CZ 0.02933 0.40193 5.17928
92 4MPO AMP 0.04333 0.41827 5.22876
93 4NSQ COA 0.0001013 0.51167 5.26316
94 4U9W COA 0.00001816 0.51506 5.31401
95 5W8E ADE 0.003296 0.40205 5.42986
96 2W58 ADP 0.03688 0.41136 5.44554
97 2CBZ ATP 0.00527 0.45258 5.48523
98 1S7N COA 0.0004379 0.47285 5.49451
99 4KOT CE3 0.0001412 0.43446 5.55556
100 1YRE COA 0.009864 0.41819 5.58376
101 2CNT COA 0.000003814 0.54869 5.625
102 1BOB ACO 0.000009003 0.53278 5.9375
103 1CM0 COA 0.0001949 0.50893 5.95238
104 5H86 BCO 0.00001449 0.50577 5.95238
105 4PSW COA 0.00003952 0.53672 5.99369
106 2CIX CEJ 0.02382 0.41086 6.02007
107 2VBQ BSJ 0.0001322 0.44802 6.06061
108 3L1N PLM 0.01738 0.42901 6.18557
109 3N7S 3N7 0.0253 0.43038 6.25
110 4KVX ACO 0.000007669 0.52591 6.41026
111 2B4B COA 0.0003046 0.47996 6.43275
112 2QCX PF1 0.02717 0.41918 6.46388
113 1JJ7 ADP 0.007923 0.45318 6.53846
114 3W54 RNB 0.01218 0.41386 6.68693
115 5M6N 7H9 0.02809 0.41952 6.77966
116 4E03 ADP 0.02836 0.41338 6.79612
117 1I1D COA 0.000001456 0.56652 6.8323
118 1I1D 16G 0.000003461 0.51726 6.8323
119 3UW5 MAA CHG PRO 0DQ 0.0201 0.42772 6.89655
120 2VWA PTY 0.04955 0.40374 6.93069
121 1DKU AP2 0.02723 0.4184 6.94006
122 4MTI 2DX 0.009064 0.44694 6.95652
123 2YLD CMO 0.03762 0.41179 7.08661
124 5OCA 9QZ 0.0003828 0.52897 7.14286
125 2DPY ADP 0.02082 0.42475 7.29167
126 4UCC ZKW 0.03161 0.42476 7.29614
127 2PZE ATP 0.008541 0.44821 7.42358
128 3TO7 COA 0.00005008 0.4966 7.6087
129 1TV5 N8E 0.04311 0.40746 7.67494
130 4QC6 30N 0.000332 0.4699 7.82123
131 5CXI 5TW 0.02627 0.40109 7.88177
132 3KO0 TFP 0.02052 0.43024 7.92079
133 1XZ3 ICF 0.04055 0.41274 8.04598
134 1JGU HBC 0.04505 0.40641 8.18182
135 1KUV CA5 0.0000283 0.4827 8.21256
136 5K04 COA 0.0002272 0.47706 8.23529
137 3ZJ0 ACO 0.0002325 0.46868 8.25243
138 5FVJ ACO 0.000005145 0.52827 8.43373
139 5C1M OLC 0.00005464 0.56056 8.44595
140 3UW4 MAA CHG PRO 0DQ 0.007517 0.4506 8.69565
141 1DTL BEP 0.03179 0.40349 8.69565
142 4MA6 28E 0.04453 0.40668 8.9172
143 4ONT SIA GAL BGC 0.04094 0.40484 9.30233
144 3B5J 12D 0.04122 0.40853 9.46502
145 5URY PAM 0.01702 0.43563 9.58904
146 4RI1 ACO 0.005333 0.42382 9.67742
147 2VVG ADP 0.04004 0.40963 9.71429
148 3FAL REA 0.01749 0.42047 9.77444
149 2V5E SCR 0.01094 0.44562 9.90099
150 1T5C ADP 0.02336 0.42346 10.0287
151 1CJW COT 0.00009176 0.47389 10.241
152 3P2H NOO 0.003382 0.44008 10.4478
153 5GVR LMR 0.02025 0.41794 10.6838
154 4M6T SAM 0.02899 0.41759 10.929
155 3SXN COA 0.000004866 0.55516 10.9375
156 2QQC AG2 0.04982 0.40399 11.6071
157 2IL4 COA 0.00002968 0.54268 11.6505
158 4NTX AMR 0.04275 0.41253 11.7647
159 1PUA COA 0.00001211 0.54892 12.2699
160 1QSN COA 0.00002115 0.53778 12.3457
161 1Q2D COA 0.00005962 0.52247 12.3457
162 1QSR ACO 0.00001514 0.51836 12.3457
163 1Q2C COA 0.0007814 0.45375 12.3457
164 3CM2 X23 0.03318 0.4137 13.0769
165 2JDC CAO 0.00009143 0.47395 13.6986
166 2Q4V ACO 0.00001133 0.51893 14.1176
167 2VEZ G6P 0.000000774 0.54656 14.2105
168 2VEZ ACO 0.000001958 0.53562 14.2105
169 4U00 ADP 0.005228 0.46141 14.7541
170 1BO4 COA 0.0000004243 0.65731 14.881
171 3MYZ TFX 0.007317 0.45695 15
172 5C9J DAO 0.04207 0.40064 15.1515
173 1GHE ACO 0.000003713 0.54919 15.2542
174 3DC4 ADP 0.009369 0.44356 15.407
175 3NHB ADP 0.02406 0.42368 15.6863
176 5MWE TCE 0.02213 0.42331 16.0494
177 1N71 COA 0.00008144 0.50581 16.1111
178 3UEC ALA ARG TPO LYS 0.04375 0.40826 16.4384
179 2WOR 2AN 0.02949 0.41966 17
180 2VSL MAA LYS PRO PHE 0.03844 0.40632 17.7083
181 2KIN ADP 0.009301 0.44737 18
182 2XT3 ADP 0.03883 0.41255 18.0233
183 4UA3 COA 0.00006986 0.50882 18.0412
184 5V4R MGT 0.03307 0.42586 18.5185
185 4D0N GDP 0.04142 0.401 18.9189
186 1QSM ACO 0.000004535 0.5353 19.0789
187 4AG9 COA 0.0000607 0.54678 20.6061
188 4AG9 16G 0.007696 0.43886 20.6061
189 2FT0 ACO 0.005101 0.43545 25.5319
190 1UO5 PIH 0.01519 0.42702 26.4706
191 4HBM 0Y7 0.02527 0.41218 26.6667
192 3F8K COA 0.000009353 0.53208 28.75
Pocket No.: 2; Query (leader) PDB : 2YNC; Ligand: YNC; Similar sites found: 11
This union binding pocket(no: 2) in the query (biounit: 2ync.bio1) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4J24 EST 0.03634 0.40053 0.833333
2 1TL2 NDG 0.03923 0.40971 2.11864
3 1YRX FMN 0.02589 0.40139 2.47934
4 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 0.04605 0.40211 2.95082
5 3SQP 3J8 0.04896 0.40781 4.16667
6 1MZV AMP 0.04024 0.40165 5.95745
7 3B9Q MLI 0.02497 0.40735 5.96026
8 2UW1 GVM 0.04479 0.41014 8.87574
9 1XVB 3BR 0.02675 0.4109 10
10 4MA7 P2Z 0.04854 0.41006 10.3286
11 3PQC GDP 0.04902 0.40438 11.2821
Pocket No.: 3; Query (leader) PDB : 2YNC; Ligand: YNC; Similar sites found: 8
This union binding pocket(no: 3) in the query (biounit: 2ync.bio3) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3WJO IPE 0.04694 0.40896 2.07715
2 4EUO ABU 0.04987 0.40247 4.375
3 3TTM PUT 0.03598 0.40743 6.35838
4 1QJI PKF 0.02353 0.40341 6.5
5 3A3B FMN 0.04555 0.40236 8.42105
6 3A3B RBF 0.04652 0.40187 8.42105
7 2XRH NIO 0.02713 0.41475 10
8 5C83 4YN 0.04486 0.40272 15.4545
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