Receptor
PDB id Resolution Class Description Source Keywords
4I4Z 2 Å EC: 4.1.3.36 SYNECHOCYSTIS SP. PCC 6803 1,4-DIHYDROXY-2-NAPHTHOYL-COENZYM SYNTHASE (MENB) IN COMPLEX WITH SALICYLYL-COA SYNECHOCYSTIS SP. CROTONASE 14-DIHYDROXY-2-NAPHTHOYL COENZYME A SYNTHASE LY
Ref.: STRUCTURAL BASIS OF THE INDUCED-FIT MECHANISM OF 1,4-DIHYDROXY-2-NAPHTHOYL COENZYME A SYNTHASE FROM CROTONASE FOLD SUPERFAMILY PLOS ONE V. 8 63095 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2NE G:301;
C:301;
H:301;
B:301;
D:301;
A:301;
I:301;
F:301;
E:301;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
887.64 C28 H40 N7 O18 P3 S CC(C)...
BCT F:302;
D:302;
I:302;
G:302;
A:302;
C:302;
H:302;
E:302;
B:302;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
61.017 C H O3 C(=O)...
MLI I:303;
C:303;
Invalid;
Invalid;
none;
none;
submit data
102.046 C3 H2 O4 C(C(=...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4I4Z 2 Å EC: 4.1.3.36 SYNECHOCYSTIS SP. PCC 6803 1,4-DIHYDROXY-2-NAPHTHOYL-COENZYM SYNTHASE (MENB) IN COMPLEX WITH SALICYLYL-COA SYNECHOCYSTIS SP. CROTONASE 14-DIHYDROXY-2-NAPHTHOYL COENZYME A SYNTHASE LY
Ref.: STRUCTURAL BASIS OF THE INDUCED-FIT MECHANISM OF 1,4-DIHYDROXY-2-NAPHTHOYL COENZYME A SYNTHASE FROM CROTONASE FOLD SUPERFAMILY PLOS ONE V. 8 63095 2013
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4I52 - 1HA C32 H42 N7 O18 P3 S CC(C)(COP(....
2 4I4Z - 2NE C28 H40 N7 O18 P3 S CC(C)(COP(....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4I52 - 1HA C32 H42 N7 O18 P3 S CC(C)(COP(....
2 4I4Z - 2NE C28 H40 N7 O18 P3 S CC(C)(COP(....
3 4I42 - 1HA C32 H42 N7 O18 P3 S CC(C)(COP(....
4 3T88 - S0N C32 H45 N8 O20 P3 CC(C)(CO[P....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4QII - 2NE C28 H40 N7 O18 P3 S CC(C)(COP(....
2 1RJN - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
3 4QIJ Kd = 2.9 uM 1HA C32 H42 N7 O18 P3 S CC(C)(COP(....
4 3T8A - S0N C32 H45 N8 O20 P3 CC(C)(CO[P....
5 1Q51 - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
6 4I52 - 1HA C32 H42 N7 O18 P3 S CC(C)(COP(....
7 4I4Z - 2NE C28 H40 N7 O18 P3 S CC(C)(COP(....
8 4I42 - 1HA C32 H42 N7 O18 P3 S CC(C)(COP(....
9 3T88 - S0N C32 H45 N8 O20 P3 CC(C)(CO[P....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 2NE; Similar ligands found: 124
No: Ligand ECFP6 Tc MDL keys Tc
1 2NE 1 1
2 COW 0.878788 0.988764
3 BYC 0.837037 0.977528
4 ACO 0.824427 0.945055
5 CAO 0.823077 0.923913
6 BCA 0.817518 0.988764
7 3KK 0.81203 0.955556
8 COS 0.80916 0.934066
9 SOP 0.80597 0.934066
10 OXK 0.80597 0.955556
11 1VU 0.8 0.945055
12 CO6 0.8 0.955556
13 MCA 0.79562 0.945055
14 2MC 0.794118 0.914894
15 FAQ 0.791367 0.977528
16 MC4 0.789855 0.905263
17 BCO 0.788321 0.955556
18 3HC 0.788321 0.966292
19 IVC 0.788321 0.966292
20 1HE 0.788321 0.934783
21 MLC 0.788321 0.955556
22 CMC 0.786765 0.934066
23 FYN 0.785185 0.955056
24 DCA 0.784615 0.912088
25 HGG 0.784173 0.955556
26 COO 0.782609 0.955556
27 CAA 0.782609 0.966292
28 COK 0.779412 0.934066
29 1HA 0.777027 1
30 SCA 0.776978 0.955556
31 HXC 0.77305 0.934783
32 0T1 0.772727 0.933333
33 COA 0.772727 0.955056
34 IRC 0.771429 0.966292
35 1GZ 0.771429 0.945055
36 30N 0.768657 0.876289
37 TGC 0.767606 0.945055
38 4KX 0.765517 0.945652
39 SCO 0.762963 0.933333
40 A1S 0.76259 0.934066
41 CO8 0.762238 0.934783
42 GRA 0.760563 0.955556
43 3CP 0.758865 0.934066
44 COF 0.758865 0.913979
45 ETB 0.757576 0.880435
46 ST9 0.756944 0.934783
47 DCC 0.756944 0.934783
48 MYA 0.756944 0.934783
49 UCC 0.756944 0.934783
50 5F9 0.756944 0.934783
51 MFK 0.756944 0.934783
52 0FQ 0.756944 0.955556
53 AMX 0.755556 0.94382
54 4CA 0.753521 0.966667
55 2CP 0.751773 0.923913
56 CMX 0.75 0.933333
57 S0N 0.75 0.955556
58 1CZ 0.75 0.945055
59 HFQ 0.748299 0.977778
60 WCA 0.746575 0.977778
61 2KQ 0.746479 0.934783
62 4CO 0.744828 0.966667
63 FAM 0.744526 0.913043
64 FCX 0.744526 0.903226
65 HDC 0.741497 0.934783
66 MCD 0.741007 0.913043
67 HAX 0.73913 0.913043
68 CS8 0.734694 0.924731
69 YE1 0.732394 0.966292
70 YNC 0.731544 0.945055
71 SCD 0.730496 0.933333
72 UOQ 0.72973 0.913979
73 NHW 0.72973 0.913979
74 NHM 0.72973 0.913979
75 CA6 0.728571 0.85
76 01A 0.727891 0.914894
77 CIC 0.726027 0.934066
78 MRS 0.724832 0.934783
79 MRR 0.724832 0.934783
80 NMX 0.723404 0.865979
81 1CV 0.722973 0.955556
82 CA8 0.722222 0.887755
83 DAK 0.72 0.945652
84 CAJ 0.71831 0.913043
85 0ET 0.716216 0.913979
86 8Z2 0.715232 0.924731
87 COT 0.698718 0.955556
88 NHQ 0.694805 0.944444
89 CCQ 0.691275 0.914894
90 01K 0.681529 0.934066
91 CA3 0.679245 0.955556
92 UCA 0.654545 0.956044
93 93P 0.654545 0.945055
94 CO7 0.651007 0.955556
95 CA5 0.648485 0.914894
96 93M 0.64497 0.945055
97 COD 0.628571 0.94382
98 4BN 0.608939 0.915789
99 5TW 0.608939 0.915789
100 JBT 0.601093 0.916667
101 OXT 0.597765 0.93617
102 PLM COA 0.57764 0.903226
103 COA MYR 0.57764 0.903226
104 COA PLM 0.57764 0.903226
105 HMG 0.575 0.923077
106 BSJ 0.551913 0.924731
107 PAP 0.51938 0.775281
108 191 0.5 0.868687
109 RFC 0.491329 0.956044
110 SFC 0.491329 0.956044
111 PPS 0.485075 0.721649
112 ACE SER ASP ALY THR NH2 COA 0.479592 0.892473
113 A3P 0.472868 0.764045
114 0WD 0.461538 0.774194
115 PTJ 0.421769 0.833333
116 3AM 0.415385 0.752809
117 PAJ 0.413793 0.844444
118 PUA 0.412121 0.804348
119 A22 0.409722 0.797753
120 A2D 0.402985 0.786517
121 3OD 0.402685 0.788889
122 ATR 0.4 0.764045
123 SAP 0.4 0.791209
124 AGS 0.4 0.791209
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4I4Z; Ligand: 2NE; Similar sites found: 18
This union binding pocket(no: 1) in the query (biounit: 4i4z.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4NEC SAH 0.01427 0.41043 2.65152
2 3F81 STT 0.01507 0.4222 3.27869
3 5KAX RHQ 0.0343 0.40633 4.21687
4 4FMS BDP 0.03507 0.40712 5.81818
5 2GMM MAN MAN 0.0145 0.42623 5.95238
6 2GN3 MAN 0.03143 0.40775 5.95238
7 1ON3 MCA 0.001933 0.40167 6.18182
8 2QLU ADE 0.02213 0.40507 6.54545
9 1KUJ MMA 0.01397 0.42739 9.77444
10 1SG4 CO8 0.0001245 0.44945 18.4615
11 2NP9 YE1 0.0000186 0.4926 32.7273
12 4IZC 1GZ 0.000002213 0.5283 36
13 2VSU ACO 0.0000009433 0.4832 37.8182
14 2VSS ACO 0.000001584 0.47668 37.8182
15 1NZY BCA 0.00000002274 0.59199 42.3792
16 1JXZ BCA 0.00000005889 0.57645 42.7509
17 5JBX COA 0.00000004024 0.53053 45.977
18 1DUB CAA 0.000001684 0.56931 49.0421
Pocket No.: 2; Query (leader) PDB : 4I4Z; Ligand: 2NE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4i4z.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 4I4Z; Ligand: 2NE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4i4z.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4I4Z; Ligand: 2NE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4i4z.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 4I4Z; Ligand: 2NE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 4i4z.bio1) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 4I4Z; Ligand: 2NE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 4i4z.bio1) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 4I4Z; Ligand: 2NE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 4i4z.bio2) has 28 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 4I4Z; Ligand: 2NE; Similar sites found: 54
This union binding pocket(no: 8) in the query (biounit: 4i4z.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2E1A MSE 0.00008872 0.49857 None
2 1G8S MET 0.01247 0.42239 0.869565
3 2F2U M77 0.001641 0.43968 1.81818
4 1LVL FAD 0.001058 0.40596 1.81818
5 1JA9 NDP 0.001306 0.42115 1.82482
6 1PEA ACM 0.03025 0.41491 2.18182
7 1XHL NDP 0.0004115 0.40478 2.18182
8 2GN4 NDP 0.02929 0.40389 2.18182
9 3A2Y TS5 0.0009492 0.42992 2.53807
10 1E8G FAD 0.009168 0.40398 2.54545
11 4M4Q 21A 0.000144 0.4014 2.90456
12 2NCD ADP 0.002412 0.44934 2.90909
13 4HA6 FAD 0.0001791 0.42927 2.90909
14 1Z44 NPO 0.04993 0.42304 2.90909
15 1D6H COA 0.0006331 0.4127 2.90909
16 1RM0 NAI 0.001772 0.40111 2.90909
17 4E28 9MZ 0.001402 0.4667 3.27273
18 4E28 0MZ 0.0019 0.45401 3.27273
19 1SOW NAD 0.0002648 0.41025 3.27273
20 4L1F FAD 0.0004117 0.40755 3.27273
21 1RP0 AHZ 0.003824 0.40594 3.27273
22 2Q37 3AL 0.01181 0.41821 3.31492
23 3O03 NAP 0.002589 0.40447 3.63636
24 2BLE 5GP 0.003943 0.40014 3.63636
25 1V7R CIT 0.0363 0.42353 3.76344
26 1WDA BAG 0.01262 0.4075 3.8806
27 4PQG NAG 0.03753 0.40151 4
28 4IXW IXW 0.006273 0.42038 4.33071
29 3DGB MUC 0.001768 0.43336 4.36364
30 1H82 GZZ 0.0005494 0.42819 4.36364
31 1H82 FAD 0.0004605 0.42819 4.36364
32 2GSD NAD 0.0007151 0.40191 4.36364
33 3MAG 3MA 0.00144 0.50021 4.72727
34 3MAG SAH 0.001189 0.41817 4.72727
35 1VL8 NAP 0.00001096 0.4325 5.61798
36 3V1U NAD 0.000184 0.40166 5.81818
37 2GN3 MMA 0.02897 0.40886 5.95238
38 1I2B USQ 0.01886 0.40179 6.18182
39 1I2B NAD 0.01886 0.40179 6.18182
40 1I2B UPG 0.01886 0.40179 6.18182
41 1ZK7 FAD 0.001891 0.40025 6.18182
42 3S9K CIT 0.01307 0.4768 6.77966
43 2PR5 FMN 0.00206 0.41361 6.81818
44 2V6O FAD 0.003503 0.40965 8.36364
45 1WVG APR 0.00004005 0.41902 8.72727
46 2QLX RM4 0.0006979 0.48865 9.25926
47 3PA8 621 0.03843 0.40485 9.44882
48 4OYA 1VE 0.006528 0.41085 9.81818
49 3T31 FAD 0.0009868 0.41609 10.1818
50 3T31 DCQ 0.001112 0.41609 10.1818
51 1SS4 GSH 0.004046 0.48972 10.4575
52 1SS4 CIT 0.004288 0.4764 10.4575
53 1N9L FMN 0.002612 0.40992 16.5138
54 1MXI SAH 0.001524 0.41829 18.75
Pocket No.: 9; Query (leader) PDB : 4I4Z; Ligand: 2NE; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 4i4z.bio2) has 29 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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