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Receptor
PDB id Resolution Class Description Source Keywords
3GFZ 2.05 Å NON-ENZYME: OTHER KLEBSIELLA PNEUMONIAE BLRP1 PH 6 MANGANESE/CY-DIGMP COMPLEX KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIA78578 TIM-BARREL EAL DOMAIN BLUF DOMAIN HYDROLASE SIGNALING PR
Ref.: STRUCTURE AND MECHANISM OF A BACTERIAL LIGHT-REGULA CYCLIC NUCLEOTIDE PHOSPHODIESTERASE. NATURE V. 459 1015 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
C2E A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
690.411 C20 H24 N10 O14 P2 c1nc2...
FMN A:504;
B:504;
Valid;
Valid;
none;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
MN A:502;
A:503;
B:502;
B:503;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GFZ 2.05 Å NON-ENZYME: OTHER KLEBSIELLA PNEUMONIAE BLRP1 PH 6 MANGANESE/CY-DIGMP COMPLEX KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIA78578 TIM-BARREL EAL DOMAIN BLUF DOMAIN HYDROLASE SIGNALING PR
Ref.: STRUCTURE AND MECHANISM OF A BACTERIAL LIGHT-REGULA CYCLIC NUCLEOTIDE PHOSPHODIESTERASE. NATURE V. 459 1015 2009
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 3GG1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3GFZ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3GFX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 3GG1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3GFZ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3GFX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 3GG1 - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
2 3GFZ - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
3 3GFX - FMN C17 H21 N4 O9 P Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: C2E; Similar ligands found: 57
No: Ligand ECFP6 Tc MDL keys Tc
1 35G 1 0.986111
2 C2E 1 1
3 PCG 1 0.986111
4 4BW 0.806818 1
5 1YD 0.806818 1
6 5GP 5GP 0.743902 0.958904
7 4UR 0.731959 1
8 6SW 0.627907 0.944444
9 1YC 0.616162 0.972222
10 6J7 0.58427 0.934211
11 CMP 0.534091 0.902778
12 2BA 0.534091 0.916667
13 GMP 0.53012 0.828947
14 1SY 0.495575 1
15 SGP 0.483871 0.825
16 6SZ 0.483871 0.916667
17 3GP 0.478261 0.92
18 1OR 0.474747 0.741176
19 G 0.468085 0.933333
20 5GP 0.468085 0.933333
21 7CH 0.467391 0.888889
22 6SX 0.462366 0.861111
23 6JR 0.457944 0.944444
24 G2R 0.457143 0.886076
25 GPX 0.451923 0.894737
26 GP3 0.44898 0.947368
27 2GP 0.446809 0.907895
28 GP2 0.444444 0.886076
29 GDP 0.444444 0.921053
30 GNH 0.44 0.909091
31 P2G 0.4375 0.881579
32 G2P 0.436893 0.886076
33 GMV 0.431373 0.897436
34 GTP 0.431373 0.921053
35 ALF 5GP 0.431373 0.841463
36 G1R 0.427184 0.909091
37 GCP 0.427184 0.897436
38 G3D 0.423077 0.933333
39 9GM 0.423077 0.897436
40 GSP 0.423077 0.875
41 GNP 0.423077 0.897436
42 GDP AF3 0.420561 0.841463
43 G4P 0.415094 0.933333
44 GAV 0.415094 0.886076
45 P1G 0.414141 0.87013
46 Y9Z 0.410714 0.833333
47 GCP G 0.409091 0.894737
48 GDP ALF 0.407407 0.841463
49 ALF GDP 0.407407 0.841463
50 N6R 0.40708 0.831169
51 N6S 0.40708 0.831169
52 G G 0.40708 0.947368
53 G3A 0.403509 0.947368
54 YGP 0.401786 0.876543
55 GPG 0.4 0.935065
56 G5P 0.4 0.947368
57 0O2 0.4 0.933333
Ligand no: 2; Ligand: FMN; Similar ligands found: 15
No: Ligand ECFP6 Tc MDL keys Tc
1 FMN 1 1
2 RBF 0.75641 0.876712
3 RS3 0.571429 0.831169
4 FAD 0.543307 0.876543
5 FAS 0.543307 0.876543
6 FAE 0.539062 0.865854
7 LFN 0.475 0.643836
8 C3F 0.473684 0.74359
9 CF4 0.463918 0.734177
10 FAY 0.446043 0.864198
11 FNR 0.444444 0.909091
12 RFL 0.442857 0.845238
13 4LS 0.411215 0.875
14 1VY 0.406593 0.769231
15 DLZ 0.404494 0.782051
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3GFZ; Ligand: FMN; Similar sites found with APoc: 220
This union binding pocket(no: 1) in the query (biounit: 3gfz.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2VBQ BSJ None
2 4F4S EFO None
3 3D9F N6C 0.968523
4 2H7C COA 1.21065
5 4PSB GA3 1.29032
6 5ICE 2H4 1.42045
7 5ICE SAH 1.42045
8 2ZKJ ADP 1.52284
9 3TTM PUT 1.7341
10 3LDW ZOL 1.76768
11 6A0S NDP 1.80723
12 4BG1 IVL 1.80879
13 4BG1 OGA 1.80879
14 5Y02 HBX 1.86916
15 1UJ2 C5P 1.98413
16 4Y30 49L 1.9943
17 3RDE OYP 2.17918
18 2Q2Y ADP 2.17984
19 2Q2Y MKR 2.17984
20 4GCZ FMN 2.33766
21 5FYR INS 2.34899
22 3SZB I1E 2.42131
23 3HYW DCQ 2.42131
24 4KWD JF2 2.54777
25 5NBP BGC BGC BGC 2.57353
26 5TPV TYD 2.61438
27 1AUA BOG 2.7027
28 6CB2 OLC 2.73038
29 4DXJ 0M9 2.76243
30 4DXJ IPE 2.76243
31 4ASE AV9 2.83286
32 1LBT T80 2.83912
33 1NHZ 486 2.85714
34 3KB9 BTM 2.87958
35 5UR1 YY9 2.89389
36 4NZF ARB 2.90557
37 5L7G 6QE 2.95082
38 5MWY YNU 2.95082
39 5DEY 59T 3.0303
40 4A38 BZS 3.09278
41 4LSJ LSJ 3.10078
42 3SAO NKN 3.125
43 4P6X HCY 3.13725
44 4CQB MLI 3.1477
45 3LN0 52B 3.1477
46 4AG8 AXI 3.16456
47 3PVT 3HC 3.21543
48 2P4Y C03 3.2491
49 4BNU 9KQ 3.34572
50 3BEJ MUF 3.36134
51 2R40 20E 3.42205
52 3OKI OKI 3.43348
53 3P7N FMN 3.48837
54 5ICK FEZ 3.49345
55 5HCV 60R 3.50195
56 1MGP PLM 3.51438
57 4OIV XX9 3.53982
58 1BGQ RDC 3.55556
59 2A3I C0R 3.55731
60 6EOZ 58K 3.57143
61 5Z1N PEF 3.57143
62 1VPV PLM 3.66667
63 3P3G 3P3 3.66667
64 3P3G UKW 3.66667
65 2GWH PCI 3.69128
66 5NM7 GLY 3.7594
67 5WGQ EST 3.83142
68 5DXG EST 3.83142
69 3BGD PM6 3.84615
70 5LX9 OLB 3.87409
71 4MG9 27K 3.92157
72 5UWA 8ND 3.94089
73 2BJ4 OHT 3.96825
74 5AAV GW5 3.96825
75 1NYW DAU 4.06091
76 3EYK EYK 4.06977
77 5K52 OCD 4.15094
78 2E56 MYR 4.16667
79 3SFI 3SF 4.23729
80 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 4.25532
81 3OJF IMJ 4.28016
82 6HOY TSN 4.30464
83 2YVE MBT 4.32432
84 3NVD OAN 4.35835
85 1N13 AG2 4.42478
86 5B4B LP5 4.43548
87 2QQC AG2 4.46429
88 2E2R 2OH 4.5082
89 2WKQ FMN 4.51807
90 2O5L MNR 4.57516
91 2HZL PYR 4.65753
92 1YOK P6L 4.6875
93 5C1M OLC 4.72973
94 4ORR PE3 4.73684
95 6GBV FMN 4.79452
96 3W5N RAM 4.84262
97 4LY9 S6P 4.86656
98 4LY9 1YY 4.86656
99 5UNJ RJW 4.89796
100 1FFU FAD 4.90798
101 1XX4 BAM 4.98084
102 5UC4 83S 5
103 5NLD LBT 5.03597
104 3SCM LGN 5.05051
105 1TV5 N8E 5.08475
106 5CKS GAL 5.12821
107 4E2J MOF 5.2
108 1R6N 434 5.21327
109 4Q0A 4OA 5.29801
110 5LGA 6VH 5.33333
111 3RUG DB6 5.39216
112 2Z6C FMN 5.42636
113 4S15 4D8 5.46875
114 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 5.47945
115 1N9L FMN 5.50459
116 2BP1 FLC 5.55556
117 2Z7I 742 5.58824
118 6B5G CQY 5.81114
119 6B5G NAD 5.81114
120 2CIX CEJ 5.81114
121 5NTW 98N 5.83658
122 4RC8 STE 5.85586
123 2O3Z AI7 5.90406
124 3GZ9 D32 5.94796
125 1DTL BEP 6.21118
126 2H12 OAA 6.2954
127 5NTP 98E 6.30252
128 4C2V YJA 6.31579
129 1XZ3 ICF 6.32184
130 4WGF HX2 6.34146
131 3E70 GDP 6.40244
132 3RLF MAL 6.41892
133 3B9Z CO2 6.4433
134 5OO5 UUA 6.45161
135 1SR7 MOF 6.56371
136 2HHP FLC 6.77966
137 2GJ5 VD3 6.79012
138 5J6A P46 7
139 1ZT1 PHE GLU ALA ASN GLY ASN LEU ILE 7.22022
140 3NB0 G6P 7.26392
141 4PGK Y69 7.37705
142 4ZGM 32M 7.37705
143 1Q6O LG6 7.40741
144 4XCP PLM 7.64706
145 1LEK GLU GLN TYR LYS PHE TYR SER VAL 7.66423
146 3QUZ QUV 7.7193
147 6A5Y 9CR 7.98319
148 6A5Y 9R0 7.98319
149 1T0S BML 8.13953
150 2AX9 BHM 8.20312
151 4M8E 29V 8.22511
152 1NU4 MLA 8.24742
153 2PR5 FMN 8.33333
154 3H0A D30 8.33333
155 3H0A 9RA 8.33333
156 4MRP GSH 8.46906
157 3E2M E2M 8.64865
158 3N7S 3N7 8.69565
159 5OCA 9QZ 8.73016
160 4A7W GTP 8.75
161 5CHR 4NC 8.75912
162 1UO5 PIH 8.82353
163 1UO4 PIH 8.82353
164 4FC7 NAP 9.02527
165 4FC7 COA 9.02527
166 5H9Q TD2 9.03226
167 4QWT ACD 9.20097
168 5LJ0 6XX 9.23077
169 3KP6 SAL 9.27152
170 4URG C2E 9.58084
171 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 9.92908
172 3WYJ H78 10.6719
173 3TL1 JRO 10.6918
174 2Z6D FMN 10.7692
175 2BHW NEX 10.7759
176 4BH1 SIA GAL NAG 10.8434
177 1N46 PFA 10.8527
178 1JGS SAL 10.8696
179 4Z24 FAD 10.8959
180 2P7Q GG6 11.2782
181 5W7B MYR 11.3475
182 4X6F 3XU 11.4286
183 4WUJ FMN 11.5646
184 2ZCQ B65 11.6041
185 4O4Z N2O 11.6883
186 4RW3 TDA 11.9205
187 4RW3 PLM 11.9205
188 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 12
189 3QFJ LEU LEU PHE GLY PHE PRO VAL TYR VAL 12
190 5C0C ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 12
191 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 12
192 1OGA GLY ILE LEU GLY PHE VAL PHE THR LEU 12
193 3QDJ ALA ALA GLY ILE GLY ILE LEU THR VAL 12
194 5WL1 CUY 12.1212
195 5U98 1KX 12.1212
196 6BJ3 ILE PRO LEU THR GLU GLU ALA GLU LEU 12.1212
197 5ISZ GLY ILE LEU GLY PHE VAL PHE THR LEU 12.2449
198 3PFG TLO 13.6882
199 3PFG SAM 13.6882
200 4YUS FMN 13.8743
201 5IVX ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 13.9175
202 5MBC FMN 14.4476
203 4XYB NDP 15.3453
204 3JZB 4HY 15.3558
205 1NF8 BOG 15.4589
206 3T50 FMN 15.625
207 2Y69 CHD 15.873
208 2HPL ASP ASP LEU TYR GLY 16
209 1ZEI CRS 16.9811
210 2Z77 HE7 17.9856
211 5ZCO CHD 21.2766
212 5Z84 CHD 21.2766
213 5W97 CHD 21.2766
214 4R38 RBF 21.4286
215 4EES FMN 23.4783
216 2D5X L35 26.2411
217 2HFN FMN 35.9477
218 2IYG FMN 37.9032
219 1YRX FMN 38.843
220 1X0P FAD 39.1608
Pocket No.: 2; Query (leader) PDB : 3GFZ; Ligand: C2E; Similar sites found with APoc: 33
This union binding pocket(no: 2) in the query (biounit: 3gfz.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 5L2R MLA 1.21065
2 4UBS DIF 2.03562
3 5FPE 3TR 2.06718
4 3GNP SOG 2.66344
5 3B0P FMN 2.85714
6 3N9R TD3 2.9316
7 2IXC TRH 2.9703
8 1VHZ APR 3.0303
9 1GVF PGH 3.14685
10 2FJK 13P 3.27869
11 1TLG GAL 4
12 3GLC R5P 4.74576
13 2Q1A 2KT 4.77816
14 3THR C2F 5.11945
15 2WDB NAG MAN 5.72917
16 6B74 BEN 5.76132
17 6GNO XDI 5.92593
18 5A04 BGC 6.78466
19 3QDV NDG 6.99301
20 3QDX CBS 6.99301
21 4WQQ MAN 7.80142
22 6D50 GCB 7.99031
23 4NAE 1GP 8
24 3NZ1 3NY 8.81226
25 1PVC ILE SER GLU VAL 10.2941
26 3HCH RSM 11.6438
27 4LJ3 C2E 22.2222
28 3HV8 C2E 25
29 3N3T C2E 26.3923
30 5MF5 C2E 26.9531
31 5MKG C2E 27.1654
32 5M1T C2E 28.4698
33 3PJU C2E 30.1205
Pocket No.: 3; Query (leader) PDB : 3GFZ; Ligand: C2E; Similar sites found with APoc: 11
This union binding pocket(no: 3) in the query (biounit: 3gfz.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 5ZQS XYP 1.45278
2 1RTF BEN 2.77778
3 5U75 SIA GAL NDG FUC 3.57143
4 1RL4 BRR 3.7234
5 4RHS SIA SIA GAL 4.09836
6 2WD7 VGD 4.10448
7 3K0T BGC 4.1958
8 5D4Y BXP 5.07042
9 4DXG NDG FUC SIA GAL 5.39216
10 5WHT SIA GAL 7.24638
11 5WHT SIA 7.24638
Pocket No.: 4; Query (leader) PDB : 3GFZ; Ligand: FMN; Similar sites found with APoc: 73
This union binding pocket(no: 4) in the query (biounit: 3gfz.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3KDU NKS None
2 3D9F FAD 0.968523
3 4JD3 COA 1.41643
4 4JD3 PLM 1.41643
5 4O1Z MXM 1.45278
6 2ABS ACP 1.56658
7 4OB6 S2T 1.75953
8 1VHT BA3 1.83486
9 5OJI ISN 1.92308
10 2EA1 GPG 2.04082
11 4MP8 MLI 2.0649
12 4MP8 NAD 2.0649
13 4U0I 0LI 2.22222
14 1PZO CBT 2.28137
15 2FTB OLA 2.4
16 3UA1 08Y 2.42131
17 4X8D AVI 2.66344
18 2FAH MLA 2.66344
19 3VHE 42Q 2.78552
20 1JV1 UD1 2.90557
21 3T58 FAD 2.90557
22 3B00 16A 2.94118
23 1M2Z DEX 3.11284
24 2HFP NSI 3.19149
25 3G9E RO7 3.32103
26 3WDX BGC BGC GLC 3.3557
27 6AYI C3G 3.51759
28 4I90 CHT 3.63036
29 1I06 TZL 3.63196
30 3STD MQ0 3.63636
31 3BJC WAN 3.87409
32 3KA2 2NC 3.94089
33 2QE4 JJ3 4.03226
34 1Z6K OAA 4.09556
35 6B9T 2HE 4.11622
36 2V6K TGG 4.20561
37 3RGA LSB 4.24028
38 3KFC 61X 4.34783
39 2P1C GG3 4.35897
40 4CRL C1I 4.5614
41 4QEK GLC 4.65116
42 4JZB P2H 4.69613
43 2R5V HHH 4.7619
44 2VHW NAI 4.77454
45 4B7P 9UN 4.78261
46 2YI0 YI0 4.80349
47 3IAE D7K 4.84262
48 3EKK GS2 4.88599
49 2JEV NHQ 5.17241
50 4D06 NAR 5.30035
51 2Q0D ATP 5.38244
52 3ROE THM 5.66038
53 3NUG NAD 5.66802
54 6EXF LYS 5.91398
55 2I0G I0G 6.61479
56 5N87 N66 6.70927
57 2V5E SCR 7.92079
58 1FM9 570 7.98319
59 3HQP OXL 7.99031
60 4POJ 2VP 8.22511
61 2P3B 3TL 9.09091
62 3GGU 017 9.09091
63 1ZOY UQ1 9.12698
64 2P3C 3TL 10.101
65 1D5Z ACE ALC ARG ALA ODA SER LEU NH2 10.4972
66 4D52 GIV 12.0635
67 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 12.2449
68 3BPX SAL 13.5135
69 2XUA SHF 13.5338
70 2OI9 GLN LEU SER PRO PHE PRO PHE ASP LEU 15.0442
71 4WO4 JLS 15.6934
72 4JX1 CAM 15.9292
73 5UGW GSH 16.5714
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