Receptor
PDB id Resolution Class Description Source Keywords
5W3Y 2.2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF POPP2 C321A IN COMPLEX WITH IP6 AND ACC RALSTONIA SOLANACEARUM POPP2 IP6 ACCOA YOPJ EFFECTOR TRANSFERASE
Ref.: MECHANISM OF HOST SUBSTRATE ACETYLATION BY A YOPJ F EFFECTOR. NAT PLANTS V. 3 17115 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACO D:502;
A:502;
C:502;
B:502;
Valid;
Valid;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0.392;
Atoms found LESS than expected: % Diff = 0.392;
Atoms found LESS than expected: % Diff = 0.392;
Atoms found LESS than expected: % Diff = 0.392;
Kd = 57.2 uM
809.571 C23 H38 N7 O17 P3 S CC(=O...
IHP D:501;
A:501;
B:501;
C:501;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
660.035 C6 H18 O24 P6 C1(C(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5W3Y 2.2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF POPP2 C321A IN COMPLEX WITH IP6 AND ACC RALSTONIA SOLANACEARUM POPP2 IP6 ACCOA YOPJ EFFECTOR TRANSFERASE
Ref.: MECHANISM OF HOST SUBSTRATE ACETYLATION BY A YOPJ F EFFECTOR. NAT PLANTS V. 3 17115 2017
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5W3T - IHP C6 H18 O24 P6 C1(C(C(C(C....
2 5W3Y Kd = 57.2 uM ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 5W3T - IHP C6 H18 O24 P6 C1(C(C(C(C....
2 5W3Y Kd = 57.2 uM ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 5W3T - IHP C6 H18 O24 P6 C1(C(C(C(C....
2 5W3Y Kd = 57.2 uM ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ACO; Similar ligands found: 170
No: Ligand ECFP6 Tc MDL keys Tc
1 ACO 1 1
2 3KK 0.9 0.988636
3 COS 0.898305 0.944444
4 CAO 0.898305 0.934066
5 2MC 0.893443 0.945652
6 OXK 0.892562 0.966292
7 MC4 0.887097 0.935484
8 1VU 0.885246 0.977528
9 CO6 0.885246 0.988636
10 CAA 0.879032 0.977273
11 SOP 0.877049 0.966292
12 IVC 0.870968 0.977273
13 1HE 0.870968 0.966667
14 MLC 0.870968 0.966292
15 BCO 0.870968 0.966292
16 3HC 0.870968 0.977273
17 FYN 0.868852 0.965909
18 COO 0.864 0.966292
19 MCA 0.864 0.977528
20 COK 0.861789 0.944444
21 0T1 0.857143 0.94382
22 SCA 0.857143 0.966292
23 COA 0.857143 0.965909
24 DCA 0.855932 0.94382
25 CMC 0.854839 0.944444
26 30N 0.85124 0.885417
27 HGG 0.850394 0.966292
28 IRC 0.850394 0.977273
29 BYC 0.850394 0.966292
30 COW 0.850394 0.955556
31 1GZ 0.850394 0.955556
32 BCA 0.84375 0.955556
33 FAQ 0.84375 0.966292
34 2CP 0.84252 0.955556
35 A1S 0.84127 0.966292
36 ETB 0.840336 0.932584
37 GRA 0.837209 0.966292
38 HXC 0.837209 0.988764
39 AMX 0.836066 0.954545
40 TGC 0.830769 0.955556
41 SCO 0.829268 0.94382
42 CMX 0.829268 0.94382
43 1CZ 0.824427 0.955556
44 CO8 0.824427 0.988764
45 2NE 0.824427 0.945055
46 FAM 0.822581 0.923077
47 FCX 0.822581 0.913043
48 2KQ 0.821705 0.988764
49 COF 0.821705 0.923913
50 3CP 0.821705 0.944444
51 UCC 0.818182 0.988764
52 ST9 0.818182 0.988764
53 DCC 0.818182 0.988764
54 MFK 0.818182 0.988764
55 5F9 0.818182 0.988764
56 MYA 0.818182 0.988764
57 HAX 0.816 0.923077
58 4CA 0.815385 0.934066
59 WCA 0.80597 0.945055
60 CS8 0.80597 0.977778
61 SCD 0.804688 0.94382
62 CA6 0.80315 0.896907
63 MCD 0.80315 0.966292
64 4KX 0.8 0.934783
65 HDC 0.8 0.988764
66 CIC 0.796992 0.944444
67 NMX 0.796875 0.875
68 MRS 0.794118 0.988764
69 MRR 0.794118 0.988764
70 4CO 0.791045 0.934066
71 0FQ 0.791045 0.944444
72 CAJ 0.790698 0.944444
73 YNC 0.788321 0.955556
74 DAK 0.788321 0.934783
75 01A 0.785185 0.904255
76 0ET 0.785185 0.966667
77 8Z2 0.782609 0.977778
78 HFQ 0.781022 0.923913
79 1CV 0.779412 0.966292
80 YE1 0.778626 0.933333
81 NHM 0.773723 0.966667
82 NHW 0.773723 0.966667
83 UOQ 0.773723 0.966667
84 CA8 0.766917 0.877551
85 1HA 0.760563 0.945055
86 NHQ 0.746479 0.955056
87 S0N 0.744526 0.923077
88 CCQ 0.744526 0.945652
89 01K 0.743056 0.966292
90 COT 0.737931 0.944444
91 CA3 0.727891 0.944444
92 UCA 0.721854 0.988764
93 CO7 0.713235 0.966292
94 CA5 0.703947 0.904255
95 93P 0.699346 0.934066
96 COD 0.692913 0.954545
97 93M 0.666667 0.934066
98 4BN 0.656627 0.946237
99 5TW 0.656627 0.946237
100 OXT 0.634731 0.946237
101 HMG 0.62585 0.933333
102 PLM COA 0.61745 0.955556
103 COA MYR 0.61745 0.955556
104 COA PLM 0.61745 0.955556
105 JBT 0.609195 0.926316
106 BSJ 0.594118 0.913979
107 PAP 0.577586 0.784091
108 PPS 0.53719 0.729167
109 191 0.532895 0.877551
110 RFC 0.53125 0.966667
111 SFC 0.53125 0.966667
112 A3P 0.525862 0.772727
113 ACE SER ASP ALY THR NH2 COA 0.505435 0.923077
114 0WD 0.503497 0.763441
115 PTJ 0.462687 0.842697
116 3AM 0.461538 0.761364
117 3OD 0.451852 0.797753
118 A22 0.450382 0.786517
119 PUA 0.447368 0.793478
120 A2D 0.446281 0.775281
121 PAJ 0.443609 0.853933
122 ATR 0.440945 0.772727
123 AGS 0.440945 0.8
124 SAP 0.440945 0.8
125 OAD 0.437037 0.797753
126 ADP 0.435484 0.795455
127 A2R 0.431818 0.786517
128 BA3 0.427419 0.775281
129 NA7 0.426471 0.829545
130 ATP 0.425197 0.795455
131 AP5 0.424 0.775281
132 B4P 0.424 0.775281
133 ADQ 0.422222 0.777778
134 5FA 0.421875 0.795455
135 AR6 0.421875 0.775281
136 APR 0.421875 0.775281
137 AQP 0.421875 0.795455
138 2A5 0.421875 0.818182
139 48N 0.42069 0.802198
140 AN2 0.420635 0.786517
141 FYA 0.42029 0.786517
142 M33 0.417323 0.786517
143 SRP 0.413534 0.808989
144 ANP 0.412214 0.777778
145 YLB 0.412162 0.877778
146 FA5 0.411348 0.788889
147 YLP 0.410959 0.877778
148 ME8 0.410072 0.835165
149 APU 0.409396 0.76087
150 5AL 0.409091 0.786517
151 7D3 0.408 0.766667
152 NJP 0.407895 0.78022
153 AD9 0.407692 0.777778
154 25L 0.407143 0.786517
155 7D4 0.40625 0.766667
156 CA0 0.40625 0.777778
157 ATF 0.406015 0.769231
158 A A A 0.405797 0.786517
159 A2P 0.404762 0.761364
160 8QN 0.404412 0.786517
161 LAQ 0.40411 0.815217
162 NDP 0.403974 0.763441
163 ACP 0.403101 0.797753
164 ACQ 0.401515 0.797753
165 YAP 0.401408 0.78022
166 ATP A A A 0.401408 0.744444
167 1ZZ 0.4 0.855556
168 PAX 0.4 0.768421
169 TXA 0.4 0.788889
170 NB8 0.4 0.782609
Ligand no: 2; Ligand: IHP; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 I6P 1 1
2 IHP 1 1
3 IP5 0.652174 1
4 5MY 0.652174 1
5 I5P 0.652174 1
6 5IP 0.652174 1
7 I0P 0.608696 0.965517
8 I7P 0.6 0.965517
9 I8P 0.6 0.965517
10 2YN 0.6 0.965517
11 I4P 0.571429 1
12 5A2 0.555556 0.8
13 5A3 0.555556 0.8
14 4WZ 0.555556 0.8
15 2IP 0.545455 0.933333
16 4IP 0.538462 0.965517
17 ITP 0.52 0.933333
18 IP2 0.5 0.933333
19 I3S 0.481481 0.933333
20 I3P 0.481481 0.933333
21 I4D 0.48 0.9
22 0EJ 0.46875 0.823529
23 4WY 0.454545 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5W3Y; Ligand: ACO; Similar sites found: 44
This union binding pocket(no: 1) in the query (biounit: 5w3y.bio2) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2O4N TPV 0.02774 0.40841 None
2 3GGU 017 0.03382 0.40509 None
3 3T3C 017 0.03771 0.40315 None
4 4NJS G08 0.04264 0.40313 None
5 2FXD DR7 0.04171 0.40043 None
6 3MDV CL6 0.02784 0.41606 1.70455
7 4UCI SAM 0.01868 0.41343 1.70455
8 3NW7 LGV 0.04801 0.41135 1.9544
9 4ORM FMN 0.0114 0.46182 1.98864
10 4ORM 2V6 0.0114 0.46182 1.98864
11 4ORM ORO 0.0114 0.46182 1.98864
12 4ITU 1HS 0.01917 0.43244 2.23048
13 2Q3O FMN 0.02927 0.40598 2.84091
14 4H6Q FAD 0.01729 0.4168 2.88462
15 1O2D NAP 0.04545 0.4091 3.125
16 2I4O ATP 0.008801 0.41727 3.40909
17 1KJ1 MAN 0.014 0.40994 3.66972
18 3CXO 1N5 0.01567 0.40644 3.69318
19 3G5D 1N1 0.02952 0.43262 4.1958
20 4OYA 1VE 0.04518 0.42103 4.26136
21 3LXK MI1 0.0396 0.40186 4.28135
22 1S7G APR 0.01955 0.42712 4.34783
23 1S7G NAD 0.01831 0.42272 4.34783
24 2BD0 NAP 0.04761 0.4019 4.5082
25 12AS AMP 0.03449 0.40313 4.54545
26 5TPR NAD 0.02279 0.41946 4.82955
27 5NE5 KIF 0.02169 0.40076 4.82955
28 1T3Q MCN 0.04002 0.4076 5.96591
29 2WKV COA 0.01771 0.4273 6.25
30 2WKT COA 0.01214 0.42208 6.25
31 2PA4 UPG 0.04917 0.40173 6.50155
32 1TIW FAD 0.0141 0.43449 6.53409
33 1TIW TFB 0.0141 0.43449 6.53409
34 4XB2 HSE 0.01547 0.42927 6.53409
35 4NMC 2OP 0.02465 0.41796 6.53409
36 4NMC FAD 0.02564 0.41796 6.53409
37 2ZE7 AMP 0.01152 0.42731 7.50988
38 2MSB NAG BMA MAN MAN MAN MAN MAN 0.01713 0.40477 7.82609
39 4O9C COA 0.01485 0.4158 8.90585
40 1SU2 ATP 0.01513 0.40849 9.43396
41 4W9F 3JU 0.008641 0.41153 15.4639
42 4B9K TG0 0.01215 0.40608 15.4639
43 3CX8 GSP 0.02894 0.4092 16.7488
44 3U7S 017 0.02714 0.40679 18.1818
Pocket No.: 2; Query (leader) PDB : 5W3Y; Ligand: IHP; Similar sites found: 11
This union binding pocket(no: 2) in the query (biounit: 5w3y.bio2) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WG0 CHD 0.006325 0.41608 None
2 4GFD 0YB 0.01718 0.41115 2.43902
3 4DHY GLC 0.02386 0.41184 2.55682
4 5GVL PLG 0.036 0.41163 2.55682
5 5GVL GI8 0.036 0.41163 2.55682
6 1YMT DR9 0.03456 0.40099 3.25203
7 4NMC FAD 0.02655 0.41688 6.53409
8 4NMC 2OP 0.02545 0.41688 6.53409
9 3G08 FEE 0.03705 0.42037 11.1111
10 3JRS A8S 0.01855 0.40631 12.0192
11 3KDJ A8S 0.01836 0.40311 12.3762
Pocket No.: 3; Query (leader) PDB : 5W3Y; Ligand: ACO; Similar sites found: 22
This union binding pocket(no: 3) in the query (biounit: 5w3y.bio4) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4MCC 21X 0.03067 0.40077 1.21951
2 5D9O BGC BGC BGC BGC 0.03366 0.40749 2.84091
3 5JKG 6LF 0.01515 0.43933 2.89389
4 1SIV PSI 0.01817 0.42294 3.0303
5 2WSB NAD 0.006986 0.44957 3.14961
6 3FWY ADP 0.02685 0.40093 3.40909
7 2DX7 CIT 0.01028 0.41634 3.50877
8 4B98 PXG 0.02125 0.40099 3.97727
9 2ZCQ B65 0.04182 0.40964 4.43686
10 5X2Z 3LM 0.01085 0.42459 4.54545
11 1XSE NDP 0.02659 0.41292 4.74576
12 4OIT MAN 0.007571 0.42211 5.30973
13 4OIT BMA 0.008402 0.41677 5.30973
14 5M58 SAH 0.031 0.40677 5.65217
15 2C1X UDP 0.04439 0.40624 5.68182
16 3CH6 311 0.04624 0.41285 6.29371
17 3CH6 NAP 0.04624 0.41285 6.29371
18 1KSH GDP 0.02207 0.40457 6.57895
19 2ZE7 DST 0.004048 0.45463 7.50988
20 1V3S ATP 0.0181 0.41434 7.75862
21 1CJW COT 0.03389 0.40656 9.03614
22 1W0H AMP 0.01334 0.41248 10.2941
Pocket No.: 4; Query (leader) PDB : 5W3Y; Ligand: IHP; Similar sites found: 6
This union binding pocket(no: 4) in the query (biounit: 5w3y.bio4) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZCQ B65 0.04411 0.41321 4.43686
2 2QM9 TDZ 0.02525 0.40367 4.51613
3 1YOK P6L 0.03421 0.41297 7.03125
4 1YUC EPH 0.02286 0.41046 7.05882
5 5OCA 9QZ 0.01444 0.40553 14.2857
6 4P6X HCY 0.04362 0.40409 18.0392
Pocket No.: 5; Query (leader) PDB : 5W3Y; Ligand: ACO; Similar sites found: 4
This union binding pocket(no: 5) in the query (biounit: 5w3y.bio3) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3KA2 2NC 0.04511 0.41313 2.46305
2 4QOM PYG 0.02264 0.40463 3.125
3 4B52 RDF 0.02578 0.40202 3.28947
4 2Y8L AMP 0.04792 0.41423 8.18182
Pocket No.: 6; Query (leader) PDB : 5W3Y; Ligand: IHP; Similar sites found: 3
This union binding pocket(no: 6) in the query (biounit: 5w3y.bio3) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5MW4 5JU 0.04641 0.40093 2.99401
2 4UP3 NDP 0.02585 0.40059 3.50318
3 2GBB CIT 0.01264 0.40271 7.69231
Pocket No.: 7; Query (leader) PDB : 5W3Y; Ligand: IHP; Similar sites found: 5
This union binding pocket(no: 7) in the query (biounit: 5w3y.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3G5D 1N1 0.02952 0.42989 4.1958
2 1TIW FAD 0.04663 0.40841 6.53409
3 1TIW TFB 0.04663 0.40841 6.53409
4 5JO1 6LM 0.01944 0.40789 12.973
5 3QM1 ZYC 0.0128 0.40728 18.1132
Pocket No.: 8; Query (leader) PDB : 5W3Y; Ligand: ACO; Similar sites found: 2
This union binding pocket(no: 8) in the query (biounit: 5w3y.bio1) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4DHY GLC 0.04191 0.40682 2.55682
2 4C0R GDS 0.03074 0.40399 6.45161
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