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Receptor
PDB id Resolution Class Description Source Keywords
3A3B 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF LUMP COMPLEXED WITH FLAVIN MONONUCLEOTI PHOTOBACTERIUM KISHITANII LUMINOUS BACTERIA LUMAZINE PROTEIN FLAVIN MONONUCLEOTIDE LUMINESCENT PROTEIN
Ref.: CRYSTAL STRUCTURES OF THE LUMAZINE PROTEIN FROM PHOTOBACTERIUM KISHITANII IN COMPLEXES WITH THE AUT CHROMOPHORE, 6,7-DIMETHYL-8-(1'-D-RIBITYL) LUMAZINE ANALOGUES, RIBOFLAVIN AND FMN, AT HIGH RESOLUTION J.BACTERIOL. V. 192 127 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FMN B:191;
Valid;
none;
submit data
456.344 C17 H21 N4 O9 P Cc1cc...
RBF A:191;
Valid;
none;
submit data
376.364 C17 H20 N4 O6 Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3A3B 2 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF LUMP COMPLEXED WITH FLAVIN MONONUCLEOTI PHOTOBACTERIUM KISHITANII LUMINOUS BACTERIA LUMAZINE PROTEIN FLAVIN MONONUCLEOTIDE LUMINESCENT PROTEIN
Ref.: CRYSTAL STRUCTURES OF THE LUMAZINE PROTEIN FROM PHOTOBACTERIUM KISHITANII IN COMPLEXES WITH THE AUT CHROMOPHORE, 6,7-DIMETHYL-8-(1'-D-RIBITYL) LUMAZINE ANALOGUES, RIBOFLAVIN AND FMN, AT HIGH RESOLUTION J.BACTERIOL. V. 192 127 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 3A3G - DLZ C13 H18 N4 O6 CC1=C(N(C2....
2 3A35 - RBF C17 H20 N4 O6 Cc1cc2c(cc....
3 3A3B - RBF C17 H20 N4 O6 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 3A3G - DLZ C13 H18 N4 O6 CC1=C(N(C2....
2 3A35 - RBF C17 H20 N4 O6 Cc1cc2c(cc....
3 3A3B - RBF C17 H20 N4 O6 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 3A3G - DLZ C13 H18 N4 O6 CC1=C(N(C2....
2 3A35 - RBF C17 H20 N4 O6 Cc1cc2c(cc....
3 3A3B - RBF C17 H20 N4 O6 Cc1cc2c(cc....
Polypharmacology
Similar Ligands
Ligand no: 1; 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
Ligand no: 2; Ligand: RBF; Similar ligands found: 14
No: Ligand ECFP6 Tc MDL keys Tc
1 RBF 1 1
2 FMN 0.75641 0.876712
3 RS3 0.74026 0.942029
4 DLZ 0.546667 0.885714
5 1VY 0.525641 0.871429
6 C3F 0.523256 0.816901
7 LFN 0.513889 0.712121
8 CF4 0.511364 0.805556
9 FAD 0.460938 0.790123
10 FAS 0.460938 0.790123
11 FAE 0.457364 0.780488
12 RLP 0.438202 0.833333
13 FO1 0.423913 0.871429
14 HDF 0.423913 0.871429
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3A3B; Ligand: RBF; Similar sites found with APoc: 177
This union binding pocket(no: 1) in the query (biounit: 3a3b.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 3R5W F42 None
2 1FLM FMN None
3 4KXQ APR 1.57895
4 4I5I NAD 1.57895
5 5MGZ SAH 1.57895
6 5M58 SAH 1.57895
7 3CB0 FMN 1.7341
8 4WQM FAD 2.10526
9 1QX4 FAD 2.10526
10 5DF1 NAP 2.10526
11 5DF1 58X 2.10526
12 5O3N 4LU 2.63158
13 4QVB F42 2.72109
14 2D37 FMN 2.84091
15 2D37 NAD 2.84091
16 1G79 PLP 3.15789
17 1G79 FMN 3.15789
18 2FV5 541 3.15789
19 1BKC INN 3.15789
20 3GBR PRP 3.15789
21 4HCX NDP 3.15789
22 3RJ5 NAD 3.15789
23 3IAE D7K 3.15789
24 5ZZO FLC 3.15789
25 4COQ SAN 3.15789
26 1X1T NAD 3.15789
27 6BXL SAM 3.15789
28 4XJ2 FMN 3.19149
29 1I0S FMN 3.5503
30 1I0S NAP 3.5503
31 2PIA FMN 3.68421
32 1PVC ILE SER GLU VAL 3.68421
33 1F20 FAD 3.68421
34 2VNI FAD 3.68421
35 2VNI A2P 3.68421
36 4NRT 2NG 3.68421
37 1CSI CMX 3.68421
38 1CSI OAA 3.68421
39 4D42 W0I 3.68421
40 4D42 NAP 3.68421
41 5OVK NDP 3.68421
42 4PXL NAD 3.68421
43 2IU8 PLM 3.68421
44 5O0B 9FE 3.7037
45 3K87 FAD 3.78378
46 1USF FMN 3.93258
47 1USF NAP 3.93258
48 1TLL FAD 4.21053
49 4F07 FAD 4.21053
50 3BNK FMN 4.21053
51 2CND FAD 4.21053
52 5JE0 AZ8 4.21053
53 5JE0 SAH 4.21053
54 2GU8 796 4.21053
55 5X8G S0N 4.21053
56 5VKM GAL SIA 4.21053
57 6CEN ACE GLY VAL NLE ARG ILE NH2 4.21053
58 6EQS BV8 4.21053
59 1JG3 VAL TYR PRO IAS HIS ALA 4.21053
60 2WFG ZZB 4.21053
61 5CX6 CDP 4.21053
62 4NON GDP 4.21053
63 3RIY NAD 4.21053
64 3EWP APR 4.51977
65 5JCA FAD 4.73684
66 3OZV FAD 4.73684
67 3OZV ECN 4.73684
68 3W2E FAD 4.73684
69 3W2E NAD 4.73684
70 2RC5 FAD 4.73684
71 4ITU NAI 4.73684
72 5DRB 5FJ 4.73684
73 3W9F I3P 4.73684
74 1ZK4 NAP 4.73684
75 4GJ3 0XP 4.73684
76 1V2G OCA 4.73684
77 4U9U FAD 5.26316
78 5O0X FAD 5.26316
79 3JQQ FAD 5.26316
80 3JQQ A2P 5.26316
81 1A8P FAD 5.26316
82 4M52 M52 5.26316
83 2BGM NAJ 5.26316
84 3ZOK NAD 5.26316
85 1DIG NAP 5.26316
86 2IMP NAI 5.26316
87 4X5S AZM 5.26316
88 5XK9 DMA 5.26316
89 3EWR APR 5.35714
90 1RZ0 FAD 5.59006
91 1RZ1 FAD 5.59006
92 4G7A AZM 5.64516
93 2BFR ADP 5.78947
94 4EUU BX7 5.78947
95 4G1V FAD 6.31579
96 5GXU FAD 6.31579
97 5KVM THR TYR PHE ALA VAL LEU MET VAL SER 6.31579
98 6C0T EE4 6.31579
99 6CI9 NAP 6.31579
100 2ZRU FMN 6.31579
101 2JJK R15 6.31579
102 2F1K NAP 6.31579
103 3SJU NDP 6.31579
104 3HRD MCN 6.31579
105 1EP2 FAD 6.84211
106 3CLH NAD 6.84211
107 1XHL NDP 6.84211
108 3HWW AKG 7.36842
109 1DDG FAD 7.36842
110 2QTZ NAP 7.36842
111 2QTZ FAD 7.36842
112 3QFS FAD 7.36842
113 3FJO FAD 7.36842
114 3TN7 NJP 7.36842
115 4YBN FAD 7.36842
116 1YKI NFZ 7.36842
117 3O2Q PRO THR SEP PRO SER TYR 7.36842
118 4KOT CE3 7.40741
119 4RF7 ARG 7.89474
120 1DJN FMN 7.89474
121 5YLT C7N 8.42105
122 5YLT SFG 8.42105
123 2YNC YNC 8.42105
124 1XKQ NDP 8.42105
125 5UIU 8CG 8.66873
126 2VBF TPP 8.94737
127 6C6O ENG 8.94737
128 3KIF GDL 9.43396
129 3WXL ADP 9.47368
130 2EIX FAD 9.47368
131 3IWK NAD 9.47368
132 4CQM NAP 9.47368
133 5XNC N4P 9.47368
134 4DQL NAP 10
135 4DQL FAD 10
136 2BSA NAP 10
137 2BSA FAD 10
138 1S4M LUM 10
139 6GEH FAD 10.5263
140 6FP4 FAD 10.5263
141 2XNJ NAP 11.0526
142 2XNJ FAD 11.0526
143 3VO1 FAD 11.0526
144 3HY8 PLP 11.0526
145 3HY8 FMN 11.0526
146 2DQA NAG NAG NAG 11.2903
147 3ZOD HQE 11.5789
148 3ZOD FMN 11.5789
149 5YLY FAD 11.5789
150 3QFA FAD 11.5789
151 1UPF URF 12.1053
152 2ED4 FAD 12.7517
153 1A27 NAP 13.1579
154 4NBT NAD 13.6842
155 5VW2 FDA 14.7368
156 5VW2 NAP 14.7368
157 5EJ2 NAD 14.7368
158 5OGX FAD 15.2632
159 5H5J FAD 15.2632
160 1KRH FAD 16.3158
161 4B4D FAD 16.8421
162 43CA NPO 17.6991
163 3CRZ FAD 19.4737
164 3CRZ NAP 19.4737
165 1FND A2P 20.0637
166 1FND FAD 20.0637
167 1SM4 FAD 20.9459
168 4YRY NAD 21.0526
169 4YRY FAD 21.0526
170 2WPB ZZI 21.0526
171 1EWY FAD 21.4286
172 1QFY NAP 22.4026
173 1QFY FAD 22.4026
174 3MHP FAD 23.3108
175 1GAW FAD 35.2632
176 1KZL CRM 48.9474
177 4G6I RS3 49.4737
Pocket No.: 2; Query (leader) PDB : 3A3B; Ligand: FMN; Similar sites found with APoc: 191
This union binding pocket(no: 2) in the query (biounit: 3a3b.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 1FLM FMN None
2 5MT9 SRO None
3 3R5W F42 None
4 1KUV CA5 None
5 4KXQ APR 1.57895
6 3CB0 FMN 1.7341
7 1SQL GUN 2.05479
8 4WQM FAD 2.10526
9 1QX4 FAD 2.10526
10 5DF1 58X 2.10526
11 5DF1 NAP 2.10526
12 5O3N 4LU 2.63158
13 2VL8 CTS 2.63158
14 5FI3 NAP 2.63158
15 4QVB F42 2.72109
16 2D37 NAD 2.84091
17 2D37 FMN 2.84091
18 1G79 FMN 3.15789
19 1G79 PLP 3.15789
20 2V3V MGD 3.15789
21 2FV5 541 3.15789
22 3RJ5 NAD 3.15789
23 1BKC INN 3.15789
24 5ZZO FLC 3.15789
25 6BXL SAM 3.15789
26 4XJ2 FMN 3.19149
27 1I0S FMN 3.5503
28 1I0S NAP 3.5503
29 1PVC ILE SER GLU VAL 3.68421
30 1F20 FAD 3.68421
31 2VNI A2P 3.68421
32 2VNI FAD 3.68421
33 4NRT 2NG 3.68421
34 5U3B 7TD 3.68421
35 1IYK MYA 3.68421
36 2IU8 PLM 3.68421
37 5OVK NDP 3.68421
38 2PIA FMN 3.68421
39 4HMT NNV 3.68421
40 2E7Z MGD 3.68421
41 4HMT FMN 3.68421
42 5O0B 9FE 3.7037
43 3K87 FAD 3.78378
44 1USF FMN 3.93258
45 1USF NAP 3.93258
46 4F07 FAD 4.21053
47 2CND FAD 4.21053
48 3BNK FMN 4.21053
49 2GU8 796 4.21053
50 5JE0 AZ8 4.21053
51 5JE0 SAH 4.21053
52 5VKM GAL SIA 4.21053
53 1JG3 VAL TYR PRO IAS HIS ALA 4.21053
54 2WFG ZZB 4.21053
55 5CX6 CDP 4.21053
56 1TLL FAD 4.21053
57 3EWP APR 4.51977
58 3OZV FAD 4.73684
59 3OZV ECN 4.73684
60 3W2E NAD 4.73684
61 3W2E FAD 4.73684
62 2RC5 FAD 4.73684
63 4ITU NAI 4.73684
64 2Z9I GLY ALA THR VAL 4.73684
65 1ZK4 NAP 4.73684
66 5JCA FAD 4.73684
67 1OBD AMP 4.73684
68 1V2G OCA 4.73684
69 3W9F I3P 4.73684
70 4RF2 NAP 4.73684
71 1XG5 NAP 4.73684
72 5Y1G NAD 4.73684
73 5Y1G AKB 4.73684
74 3TE4 ACO 4.73684
75 4U9U FAD 5.26316
76 3JQQ FAD 5.26316
77 3JQQ A2P 5.26316
78 5O0X FAD 5.26316
79 1A8P FAD 5.26316
80 5SWB NAG BMA MAN MAN MAN MAN 5.26316
81 4M52 M52 5.26316
82 2BGM NAJ 5.26316
83 4FK7 P34 5.26316
84 1WMA NDP 5.26316
85 1WMA AB3 5.26316
86 3ZOK NAD 5.26316
87 2IMP NAI 5.26316
88 4X5S AZM 5.26316
89 1DIG NAP 5.26316
90 4ZFL 4NK 5.26316
91 3EWR APR 5.35714
92 1RZ0 FAD 5.59006
93 1RZ1 FAD 5.59006
94 4G7A AZM 5.64516
95 2BFR ADP 5.78947
96 4QTU SAM 5.92593
97 4G1V FAD 6.31579
98 5GXU FAD 6.31579
99 2JJK R15 6.31579
100 6C0T EE4 6.31579
101 6CI9 NAP 6.31579
102 2ZRU FMN 6.31579
103 3KC1 2T6 6.31579
104 3HRD FAD 6.31579
105 2F1K NAP 6.31579
106 1EP2 FAD 6.84211
107 5OJ7 AR6 6.84211
108 4O1M NAD 6.84211
109 5OJI NAP 6.84211
110 5OJI ISN 6.84211
111 1XHL NDP 6.84211
112 1T9M FMN 6.84211
113 1OZH HE3 6.84211
114 3HWW AKG 7.36842
115 2QTZ FAD 7.36842
116 2QTZ NAP 7.36842
117 1DDG FAD 7.36842
118 5FA6 FAD 7.36842
119 5FA6 FMN 7.36842
120 5FA6 NAP 7.36842
121 3QFS FAD 7.36842
122 3FJO FAD 7.36842
123 4YBN FAD 7.36842
124 3QFS NAP 7.36842
125 2DKN NAI 7.36842
126 3TN7 NJP 7.36842
127 2D4V NAD 7.36842
128 4KOT CE3 7.40741
129 4RF7 ARG 7.89474
130 1YP4 ADP 7.89474
131 1DJN FMN 7.89474
132 4XO8 KGM 8.22785
133 1XKQ NDP 8.42105
134 2YNC YNC 8.42105
135 1QSR ACO 8.64198
136 5UIU 8CG 8.66873
137 2VBF TPP 8.94737
138 6C6O ENG 8.94737
139 1Y8Q ATP 8.94737
140 3KIF GDL 9.43396
141 3WXL ADP 9.47368
142 2EIX FAD 9.47368
143 4CQM NAP 9.47368
144 5XNC MTA 9.47368
145 2BSA NAP 10
146 2BSA FAD 10
147 4DQL NAP 10
148 4DQL FAD 10
149 5WPJ NDP 10
150 6GEH FAD 10.5263
151 5B4T 3HR 10.5263
152 5B4T NAD 10.5263
153 5E5U MLI 10.5263
154 2XNJ NAP 11.0526
155 2XNJ FAD 11.0526
156 3HY8 PLP 11.0526
157 3HY8 FMN 11.0526
158 3VO1 FAD 11.0526
159 3ZOD HQE 11.5789
160 3ZOD FMN 11.5789
161 5YLY FAD 11.5789
162 3QFA FAD 11.5789
163 1UPF URF 12.1053
164 3PPM JG1 12.1053
165 3AFN NAP 12.4031
166 2ED4 FAD 12.7517
167 2HF9 GSP 13.1579
168 1A27 NAP 13.1579
169 4NBT NAD 13.6842
170 1BDB NAD 14.2105
171 5VW2 NAP 14.7368
172 5VW2 FDA 14.7368
173 5OGX FAD 15.2632
174 5H5J FAD 15.2632
175 1KRH FAD 16.3158
176 4B4D FAD 16.8421
177 3NRR D16 18.4211
178 3CRZ FAD 19.4737
179 3CRZ NAP 19.4737
180 1FND FAD 20.0637
181 1FND A2P 20.0637
182 1SM4 FAD 20.9459
183 4YRY FAD 21.0526
184 4YRY NAD 21.0526
185 1EWY FAD 21.4286
186 1QFY NAP 22.4026
187 1QFY FAD 22.4026
188 3MHP FAD 23.3108
189 1GAW FAD 35.2632
190 1KZL CRM 48.9474
191 4G6I RS3 49.4737
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