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Receptor
PDB id Resolution Class Description Source Keywords
3KYG 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VCA0042 (L135R) COMPLEXED WITH C-DI-GMP VIBRIO CHOLERAE C-DI-GMP PILZ DOMAIN PP4397 VCA0042 UNKNOWN FUNCTION
Ref.: STRUCTURE OF PP4397 REVEALS THE MOLECULAR BASIS FOR DIFFERENT C-DI-GMP BINDING MODES BY PILZ DOMAIN PROTEINS. J.MOL.BIOL. V. 398 97 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5GP 5GP A:501;
A:503;
B:501;
B:503;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 55.1 nM
688.4 n/a O=P1(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KYG 2.1 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF VCA0042 (L135R) COMPLEXED WITH C-DI-GMP VIBRIO CHOLERAE C-DI-GMP PILZ DOMAIN PP4397 VCA0042 UNKNOWN FUNCTION
Ref.: STRUCTURE OF PP4397 REVEALS THE MOLECULAR BASIS FOR DIFFERENT C-DI-GMP BINDING MODES BY PILZ DOMAIN PROTEINS. J.MOL.BIOL. V. 398 97 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3KYG Kd = 55.1 nM 5GP 5GP n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 3KYG Kd = 55.1 nM 5GP 5GP n/a n/a
2 2RDE Kd = 97.1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 3KYG Kd = 55.1 nM 5GP 5GP n/a n/a
2 2RDE Kd = 97.1 nM C2E C20 H24 N10 O14 P2 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 5GP 5GP; Similar ligands found: 44
No: Ligand ECFP6 Tc MDL keys Tc
1 5GP 5GP 1 1
2 C2E 0.743902 0.958904
3 PCG 0.743902 0.945205
4 35G 0.743902 0.945205
5 4BW 0.632653 0.958904
6 1YD 0.632653 0.958904
7 4UR 0.579439 0.958904
8 GMP 0.52381 0.815789
9 1YC 0.518868 0.931507
10 3GP 0.473118 0.906667
11 5GP 0.463158 0.894737
12 G 0.463158 0.894737
13 SGP 0.463158 0.8125
14 GDP 0.454545 0.883117
15 6SW 0.453608 0.90411
16 G1R 0.45098 0.871795
17 GP3 0.444444 0.909091
18 2GP 0.442105 0.87013
19 ALF 5GP 0.441176 0.851852
20 GP2 0.44 0.85
21 G2R 0.439252 0.85
22 GNH 0.435644 0.871795
23 6J7 0.434343 0.896104
24 P2G 0.43299 0.868421
25 G2P 0.432692 0.85
26 G3D 0.432692 0.894737
27 GTP 0.427184 0.883117
28 GMV 0.427184 0.860759
29 G4P 0.424528 0.894737
30 GCP 0.423077 0.860759
31 GPX 0.420561 0.857143
32 GNP 0.419048 0.860759
33 9GM 0.419048 0.860759
34 GSP 0.419048 0.839506
35 GDP AF3 0.416667 0.851852
36 ALF GDP 0.416667 0.851852
37 GDP ALF 0.416667 0.851852
38 GAV 0.411215 0.85
39 P1G 0.41 0.857143
40 Y9Z 0.40708 0.8
41 GCP G 0.405405 0.932432
42 G G 0.403509 0.934211
43 GH3 0.401869 0.883117
44 G3A 0.4 0.909091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KYG; Ligand: 5GP 5GP; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 3kyg.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 1IIM TTP 4.40529
2 3IAE D7K 7.04846
3 4P53 NAI 7.48899
4 5XLY C2E 14.2857
5 5Y4R C2E 17.931
Pocket No.: 2; Query (leader) PDB : 3KYG; Ligand: 5GP 5GP; Similar sites found with APoc: 8
This union binding pocket(no: 2) in the query (biounit: 3kyg.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 3A1C ACP 2.20264
2 3OZ2 FAD 3.0837
3 4NZN ANP 3.52423
4 4NZN 2OU 3.52423
5 1E3Z ACI GLD GLC ACI GLD GLC ACI GLD GLC GLC 3.96476
6 2UZ1 TPP 7.04846
7 5U3B 7TD 8.37004
8 1GPE FAD 14.978
Pocket No.: 3; Query (leader) PDB : 3KYG; Ligand: 5GP 5GP; Similar sites found with APoc: 209
This union binding pocket(no: 3) in the query (biounit: 3kyg.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 3IWD M2T None
2 4MTI 2DX None
3 4NAE 1GP 0.888889
4 5DQ8 FLF 1.32159
5 3G5D 1N1 1.76211
6 5H2U 1N1 1.76211
7 5TWB FAD 1.76211
8 4Y24 TD2 1.94805
9 1SBR VIB 2
10 5C8W PCG 2.0979
11 4QPW XYP XYP XYP 2.11268
12 3EM0 CHD 2.17391
13 4L3L 5FI 2.20264
14 4OYA 1VE 2.20264
15 5Y72 DST 2.20264
16 3GC8 B45 2.20264
17 1I7M CG 2.20264
18 1SW1 PBE 2.20264
19 5H4S RAM 2.20264
20 3IES M24 2.20264
21 4O9S 2RY 2.32558
22 3UW5 MAA CHG PRO 0DQ 2.58621
23 2Z3U CRR 2.64317
24 5XVG 8FX 2.64317
25 3I9U DTU 2.64317
26 4GID 0GH 2.64317
27 2DXU BT5 2.64317
28 4LOO SB4 2.64317
29 5KD6 6C7 2.64317
30 1WPY BTN 2.64317
31 5HCY 60D 2.64317
32 5H9Y BGC BGC BGC BGC 2.64317
33 4MIB 28M 2.64317
34 2YAK OSV 2.64317
35 5EOB 5QQ 2.64317
36 5KD6 LBU 2.64317
37 2X32 OTP 2.7933
38 1QKQ MAN 2.8169
39 2GU8 796 3.0837
40 3NKS ACJ 3.0837
41 6E1Q CFA 3.0837
42 2IVD ACJ 3.0837
43 1VRP ADP 3.0837
44 4ONA UW1 3.0837
45 1U6R ADP 3.0837
46 6MPT C30 3.0837
47 2J5B TYE 3.0837
48 5VC5 96M 3.0837
49 3HAZ NAD 3.0837
50 1GET FAD 3.0837
51 1GET NAP 3.0837
52 3EEL 53T 3.0837
53 5UIU 8CG 3.0837
54 2VSL MAA LYS PRO PHE 3.125
55 5H9P TD2 3.16456
56 4K79 GAL A2G 3.18182
57 3HCH RSM 3.42466
58 5KJW 53C 3.52423
59 3ESS 18N 3.52423
60 1G51 AMP 3.52423
61 4ZUL UN1 3.52423
62 4DQ2 BTX 3.52423
63 3LGS SAH 3.52423
64 3E9I XAH 3.52423
65 3A1I UNU 3.52423
66 2ART LPA AMP 3.52423
67 1TT8 PHB 3.65854
68 2AGC DAO 3.7037
69 5TZO 7V7 3.7234
70 3CM2 X23 3.84615
71 5OQW A4E 3.93701
72 3VRY B43 3.96476
73 3JU6 ANP 3.96476
74 3RG9 NDP 3.96476
75 1YXM ADE 3.96476
76 5F3I 5UJ 3.96476
77 5DEY 59T 3.96476
78 3JQ3 ADP 3.96476
79 3CBC DBS 4.0404
80 4F8L AES 4.13793
81 2Z9I GLY ALA THR VAL 4.32099
82 5FPE 3TR 4.40529
83 5G48 1FL 4.40529
84 4WHZ 3NL 4.40529
85 1IZC PYR 4.40529
86 3K8D KDO 4.40529
87 3IWJ NAD 4.40529
88 2HIM ASN 4.40529
89 2IU8 PLM 4.40529
90 6GNO XDI 4.44444
91 5C83 4YN 4.54545
92 2YKL NLD 4.62963
93 4MOB ADP 4.84582
94 2GQS C2R 4.84582
95 3ZJX BOG 4.84582
96 3QPB URA 4.84582
97 3VZ3 NAP 4.84582
98 3VZ3 SSN 4.84582
99 5UKL SIX 4.84582
100 3V0H I3P 4.84582
101 1ODJ GMP 4.84582
102 1HXD BTN 4.84582
103 1KDK DHT 5.08475
104 1RZX ACE VAL LYS GLU SER LEU VAL 5.10204
105 3A5Z KAA 5.2356
106 5FKP 6UL 5.28634
107 6C0T EE4 5.28634
108 3G08 FEE 5.28634
109 4LRJ ANP 5.32544
110 1OFL NGK GCD 5.72687
111 5HV7 RBL 5.72687
112 5BVE 4VG 5.72687
113 4YRI 4JH 5.72687
114 5F7U GLC GLC 5.72687
115 6GH9 MIX 5.72687
116 4LH0 GLV 5.72687
117 2I4O ATP 5.72687
118 5OCG 9R5 5.82011
119 1UYY BGC BGC 6.10687
120 4YJK URA 6.1674
121 4WOE ADP 6.1674
122 3MVH WFE 6.1674
123 1ZB6 GST 6.1674
124 5VCM UDP 6.1674
125 2JDR GLY ARG PRO ARG THR THR SER PHE ALA GLU 6.1674
126 2JDR L20 6.1674
127 5M90 JIF 6.1674
128 1B7Y FYA 6.1674
129 2GJ5 VD3 6.17284
130 4XTX 590 6.2963
131 3TCT 3MI 6.29921
132 6FA4 D1W 6.35838
133 2IDO TMP 6.45161
134 5TUF TDC 6.60793
135 2OJW ADP 6.60793
136 5IFK HPA 6.60793
137 5TUF FAD 6.60793
138 6ALW BNV 6.60793
139 6ALW BMJ 6.60793
140 2W5P CL8 6.71141
141 5HWV MBN 6.92308
142 2WLG SOP 6.97674
143 5YRV 5AD 7
144 4FE2 AIR 7.04846
145 3O2K DST 7.04846
146 1VA6 ADP 7.04846
147 1VA6 P2S 7.04846
148 5A89 FMN 7.05128
149 4YLZ LAT NAG GAL 7.18954
150 5AOG IAC 7.48899
151 4CLI 5P8 7.48899
152 3SAO DBH 7.5
153 2XG5 EC2 7.51445
154 2XG5 EC5 7.51445
155 2AG4 LP3 7.92683
156 2AG4 OLA 7.92683
157 6EWZ APC 7.92952
158 3GD9 GLC BGC BGC BGC 7.92952
159 6DZN AE3 7.9646
160 1ZNY GDP 8.69565
161 1VMK GUN 8.81057
162 3QSB 743 8.81057
163 5W4W 9WG 9.2511
164 3A16 PXO 9.2511
165 3DLG GWE 9.2511
166 4KBA 1QM 9.2511
167 5TVF CGQ 9.41177
168 1V3S ATP 9.48276
169 5XDT ZI7 9.69163
170 1FHX 4IP 10.0775
171 1GPM AMP 10.1322
172 3BJE URA 10.1322
173 4YSW FAD 10.1322
174 4YSW NAI 10.1322
175 5M6N 7H9 10.1695
176 4F7E 0SH 10.2041
177 5LYH 7B8 10.3627
178 2HO2 PRO PRO PRO PRO PRO PRO PRO PRO PRO LEU 10.5263
179 3H0L ADP 10.5727
180 6H39 FGY 10.7143
181 3EFS BTN 10.7296
182 3OV6 MK0 11.0132
183 1J3I WRA 11.0132
184 4XDA RIB 11.0132
185 4YVN EBS 11.0132
186 2VL1 GLY GLY 11.4537
187 4RF7 ARG 11.8943
188 1AOE NDP 12.5
189 1AOE GW3 12.5
190 1LSH PLD 12.7753
191 4LAE 1VM 13.1737
192 4LAE NAP 13.1737
193 1SDW IYT 13.2159
194 1F9V ADP 13.2159
195 3RUG DB6 13.2159
196 2CJU PHX 15.7025
197 3WG3 A2G GAL NAG FUC 15.7303
198 5FUI APY 16.6667
199 1VJY 460 17.1806
200 1WZ1 DNS 17.6991
201 2REG CHT 19.8238
202 5LRT ADP 20.2643
203 5CIC 51R 22.2222
204 1HFE CYS 23.5772
205 4X6F 3XU 23.8095
206 4WO4 JLS 25
207 5WL1 D3D 25.2525
208 5WL1 CUY 25.2525
209 5U98 1KX 25.2525
Pocket No.: 4; Query (leader) PDB : 3KYG; Ligand: 5GP 5GP; Similar sites found with APoc: 92
This union binding pocket(no: 4) in the query (biounit: 3kyg.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 2BL9 NDP 1.32159
2 2BL9 CP6 1.32159
3 3KVY URA 1.32159
4 4TWP AXI 1.32159
5 4WUP 3UF 1.32159
6 2XZ9 PYR 1.32159
7 3C6K SPD 1.76211
8 3C6K MTA 1.76211
9 1OSS BEN 1.79372
10 4IEN GDP 1.84049
11 2QIA U20 2.20264
12 2C49 ADN 2.20264
13 1HKK NAA NAA AMI 2.20264
14 1OUK 084 2.64317
15 1MO9 FAD 2.64317
16 1MO9 KPC 2.64317
17 6B3V 7DQ 2.64317
18 5N5U 7N8 2.64317
19 3UDZ ADP 2.64317
20 5MW4 5JU 2.64317
21 6GAR FAD 2.64317
22 6GWR FEW 3.0837
23 3LAD FAD 3.0837
24 1RE8 BD2 3.0837
25 3ORK AGS 3.0837
26 4M3P HCS 3.0837
27 4WB6 ATP 3.0837
28 4QMN DB8 3.22581
29 3UW4 MAA CHG PRO 0DQ 3.26087
30 1KRR ACO 3.44828
31 3LGS ADE 3.52423
32 1O9J NAD 3.52423
33 3PE2 E1B 3.52423
34 4I3V NAD 3.52423
35 5F7J ADE 3.52423
36 6B5G NAD 3.52423
37 3I3X U22 3.52423
38 5C5H 4YB 3.52423
39 3RG9 WRA 3.96476
40 5LIA 6XN 3.96476
41 5A3T MMK 3.96476
42 3IA4 NDP 4.32099
43 1F5F DHT 4.39024
44 2XVD AS6 4.40529
45 4NV7 COA 4.40529
46 4WNK 453 4.40529
47 4TVD BGC 4.40529
48 3WWX DIA 4.40529
49 5KOK S9T 4.40529
50 5LJB RTL 4.44444
51 4QYN RTL 4.51128
52 2QHS OCA 4.84582
53 4B0T ADP 4.84582
54 6BE3 NAG 4.84582
55 2QHV OC9 5.2381
56 4CS4 ANP 5.28634
57 5N5S NAP 5.28634
58 4NPL AKG 5.28634
59 3RHJ NAP 5.28634
60 1E1O LYS 5.28634
61 6D6L FY4 5.29412
62 4CQE CQE 5.72687
63 5U3F 7TS 5.72687
64 4XV1 904 5.72687
65 2XIQ MLC 5.72687
66 2OFV 242 6.1674
67 1XOC VAL ASP SER LYS ASN THR SER SER TRP 6.1674
68 1KGI T4A 6.29921
69 4YWV SSN 6.60793
70 3LVW GSH 6.60793
71 4J56 FAD 6.60793
72 6CC0 EWM 6.60793
73 4FFG 0U8 7.04846
74 5A89 ADP 7.05128
75 5TA6 79D 7.92952
76 1V97 FAD 7.92952
77 4X3R 686 7.92952
78 3LXK MI1 7.92952
79 2WET FAD 7.92952
80 2HPL ASP ASP LEU TYR GLY 8
81 1RM6 PCD 8.81057
82 4Z87 GDP 9.2511
83 4NG2 OHN 9.73451
84 2JLD AG1 10.5727
85 4CQM NAP 10.5727
86 1J3I NDP 11.0132
87 2RAB FAD 11.4537
88 3ZGJ RMN 11.8943
89 3SJK LYS PRO VAL LEU ARG THR ALA 12.6316
90 3TAO PGH 14.6067
91 3PVW QRX 14.8649
92 2F5Z FAD 17.1875
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