Receptor
PDB id Resolution Class Description Source Keywords
5DOZ 2.26 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF JAMJ ENOYL REDUCTASE (NADPH BOUND) LYNGBYA MAJUSCULA ENOYL REDUCTASE POLYKETIDE SYNTHASE NADPH CYCLOPROPANE OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR CYCLOPROPANATION BY A UNIQUE E CARRIER PROTEIN REDUCTASE. STRUCTURE V. 23 2213 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NDP A:502;
C:401;
B:401;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
ACT A:501;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5DOZ 2.26 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF JAMJ ENOYL REDUCTASE (NADPH BOUND) LYNGBYA MAJUSCULA ENOYL REDUCTASE POLYKETIDE SYNTHASE NADPH CYCLOPROPANE OXIDOREDUCTASE
Ref.: STRUCTURAL BASIS FOR CYCLOPROPANATION BY A UNIQUE E CARRIER PROTEIN REDUCTASE. STRUCTURE V. 23 2213 2015
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 5DOZ - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
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 5DOZ - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 5DP2 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
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 5DOZ - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
2 5DP2 - NAP C21 H28 N7 O17 P3 c1cc(c[n+]....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDP; Similar ligands found: 159
No: Ligand ECFP6 Tc MDL keys Tc
1 NDP 1 1
2 0WD 0.827273 1
3 NAI 0.803738 0.986842
4 NMN AMP PO4 0.794643 0.948052
5 NPW 0.692308 0.962025
6 NZQ 0.686441 0.987013
7 DG1 0.68 1
8 1DG 0.68 1
9 A2R 0.650943 0.909091
10 A22 0.64486 0.934211
11 TXP 0.644628 0.924051
12 ATR 0.640777 0.894737
13 NA7 0.636364 0.886076
14 XNP 0.620968 0.949367
15 AP0 0.598361 0.948718
16 A2P 0.598039 0.881579
17 NJP 0.574803 0.923077
18 25L 0.550847 0.934211
19 ODP 0.550388 0.936709
20 NAX 0.544 0.949367
21 25A 0.53913 0.921053
22 2AM 0.529412 0.87013
23 6V0 0.519685 0.974026
24 NAP 0.514493 0.922078
25 EAD 0.507143 0.949367
26 A2D 0.504673 0.921053
27 TXE 0.503876 0.935897
28 NA0 0.496454 0.910256
29 TXD 0.496124 0.911392
30 SAP 0.495575 0.875
31 AGS 0.495575 0.875
32 P1H 0.493056 0.925926
33 CO7 0.489796 0.791209
34 TAP 0.489362 0.864198
35 PAP 0.482456 0.907895
36 BA3 0.481818 0.921053
37 NAJ PZO 0.478261 0.924051
38 ATP 0.477876 0.921053
39 B4P 0.477477 0.921053
40 ADP 0.477477 0.921053
41 AP5 0.477477 0.921053
42 OAD 0.47541 0.897436
43 5FA 0.473684 0.921053
44 AR6 0.473684 0.896104
45 APR 0.473684 0.896104
46 AQP 0.473684 0.921053
47 AN2 0.473214 0.909091
48 3OD 0.467742 0.897436
49 50T 0.464912 0.884615
50 PO4 PO4 A A A A PO4 0.463415 0.857143
51 V3L 0.461538 0.896104
52 2A5 0.46087 0.85
53 A1R 0.459016 0.841463
54 ADQ 0.459016 0.897436
55 4AD 0.459016 0.875
56 OVE 0.458716 0.8375
57 OMR 0.458647 0.813953
58 PPS 0.457627 0.811765
59 AD9 0.456897 0.897436
60 CA0 0.45614 0.897436
61 M33 0.45614 0.884615
62 ADJ 0.455882 0.879518
63 A3P 0.455357 0.894737
64 ACP 0.452174 0.897436
65 ENP 0.451613 0.85
66 UP5 0.451128 0.948052
67 SRP 0.45 0.8625
68 ANP 0.449153 0.897436
69 ACQ 0.449153 0.897436
70 PRX 0.448276 0.82716
71 5AL 0.445378 0.884615
72 7D4 0.443478 0.8375
73 ADX 0.443478 0.811765
74 AMP 0.436364 0.894737
75 A 0.436364 0.894737
76 4TC 0.433824 0.924051
77 7D3 0.433628 0.8375
78 ETB 0.433566 0.797753
79 DCA 0.433566 0.788889
80 1ZZ 0.433071 0.802326
81 BIS 0.433071 0.864198
82 00A 0.432 0.864198
83 ATF 0.429752 0.886076
84 0T1 0.427586 0.788889
85 5SV 0.427419 0.788235
86 8QN 0.427419 0.884615
87 3AM 0.427273 0.857143
88 N01 0.426573 0.884615
89 PR8 0.425197 0.811765
90 WAQ 0.425197 0.841463
91 LAD 0.425197 0.821429
92 DTP 0.425 0.8375
93 AMO 0.424 0.886076
94 PAJ 0.424 0.843373
95 APC 0.423729 0.886076
96 UPA 0.423358 0.935897
97 48N 0.422222 0.853659
98 FYA 0.421875 0.860759
99 PTJ 0.421875 0.853659
100 CNA 0.421429 0.910256
101 PUA 0.42069 0.9125
102 NXX 0.419118 0.910256
103 DND 0.419118 0.910256
104 AV2 0.418033 0.848101
105 COA 0.417808 0.788889
106 3UK 0.417323 0.897436
107 OOB 0.416 0.909091
108 IVC 0.415584 0.78022
109 DAT 0.415254 0.8375
110 NDO 0.414966 0.897436
111 139 0.414286 0.901235
112 3AT 0.413223 0.896104
113 TAT 0.413223 0.886076
114 YLB 0.413043 0.784091
115 62F 0.4125 0.823529
116 ABM 0.412281 0.848101
117 YAP 0.412214 0.875
118 YLP 0.411765 0.784091
119 ME8 0.410853 0.802326
120 NB8 0.410853 0.853659
121 SON 0.410256 0.886076
122 DLL 0.409449 0.909091
123 AHX 0.409449 0.853659
124 COS 0.409396 0.771739
125 AMX 0.409396 0.797753
126 CAO 0.409396 0.763441
127 30N 0.409396 0.72449
128 7D5 0.409091 0.8125
129 4UW 0.408759 0.9125
130 APX 0.407692 0.841463
131 SRA 0.40708 0.85
132 CMX 0.406667 0.788889
133 SCO 0.406667 0.788889
134 TYM 0.405797 0.886076
135 COD 0.405594 0.777778
136 OXK 0.405229 0.771739
137 CA6 0.405229 0.70297
138 A12 0.405172 0.886076
139 AP2 0.405172 0.886076
140 9SN 0.40458 0.853659
141 LAQ 0.404412 0.802326
142 T5A 0.404255 0.914634
143 FAM 0.403974 0.771739
144 ACO 0.403974 0.763441
145 FCX 0.403974 0.763441
146 AMP MG 0.403509 0.825
147 VO4 ADP 0.403226 0.860759
148 ADP VO4 0.403226 0.860759
149 YLC 0.402878 0.823529
150 1VU 0.402597 0.763441
151 FA5 0.401515 0.886076
152 HAX 0.401316 0.771739
153 APU 0.4 0.923077
154 TXA 0.4 0.886076
155 A U 0.4 0.898734
156 4UU 0.4 0.948052
157 AFH 0.4 0.843373
158 CAJ 0.4 0.771739
159 AR6 AR6 0.4 0.871795
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5DOZ; Ligand: NDP; Similar sites found: 127
This union binding pocket(no: 1) in the query (biounit: 5doz.bio1) has 34 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZAT NAP 0.001167 0.4059 1.15385
2 3CH6 NAP 0.00551 0.41234 1.3986
3 3CH6 311 0.00551 0.41234 1.3986
4 2O4C NAD 0.0008194 0.41379 1.77515
5 4MP8 NAD 0.01413 0.40511 1.77515
6 4MP8 MLI 0.01413 0.40511 1.77515
7 1RPN NDP 0.001552 0.40637 1.79104
8 4PLT NAI 0.003272 0.41767 1.81269
9 4PLT OXM 0.006335 0.40492 1.81269
10 1GUZ NAD 0.001283 0.40296 1.93548
11 1O6Z NAD 0.0005939 0.40158 1.9802
12 3CMC NAD 0.00273 0.42719 2.09581
13 1CER NAD 0.0005849 0.44246 2.1148
14 4DPL NAP 0.0006631 0.41378 2.36686
15 4E5N NAD 0.001353 0.40637 2.36686
16 2DBZ NAP 0.001036 0.4052 2.36686
17 2A92 NAI 0.001404 0.40866 2.49221
18 1V8B NAD 0.0007802 0.42399 2.66272
19 1EBF NAD 0.0003355 0.40864 2.66272
20 2NAD NAD 0.001973 0.40795 2.66272
21 5IN4 NAP 0.04016 0.40704 2.66272
22 5IN4 GDP 0.04006 0.4063 2.66272
23 5IN4 6CK 0.04381 0.40507 2.66272
24 4BVA NDP 0.001945 0.4012 2.68657
25 1F06 2NP 0.002128 0.40553 2.8125
26 1F06 NDP 0.002128 0.40553 2.8125
27 3ABI NAD 0.0002249 0.43145 2.95858
28 3WQQ IB3 0.001477 0.41934 2.95858
29 3WQQ NDP 0.001477 0.41934 2.95858
30 5GT9 NAP 0.0004164 0.42406 3.04183
31 4XQC NAD 0.001191 0.42493 3.25444
32 4XQC 13D 0.001469 0.42247 3.25444
33 1N7G NDP 0.01355 0.40101 3.25444
34 1N7G GDR 0.009045 0.40034 3.25444
35 3V1Y NAD 0.0005924 0.40743 3.2641
36 1AE1 NAP 0.001816 0.40678 3.2967
37 4R5M 4NO 0.0004024 0.42403 3.5503
38 4R5M NAP 0.0003093 0.42045 3.5503
39 3OND NAD 0.001397 0.42614 3.84615
40 3OND ADN 0.001397 0.42614 3.84615
41 1J49 NAD 0.001381 0.40024 3.9039
42 2JAP NDP 0.001195 0.40774 4.04858
43 2ZJ1 ARJ 0.001613 0.42641 4.14201
44 2ZJ1 NAD 0.001837 0.42421 4.14201
45 3KB6 NAD 0.001093 0.40075 4.49102
46 3A4V NAD 0.002987 0.40248 4.73186
47 3A4V PYR 0.002987 0.40248 4.73186
48 5M67 3D1 0.002272 0.41892 4.73373
49 5M67 NAD 0.002338 0.41844 4.73373
50 5M67 ADE 0.00249 0.41739 4.73373
51 1J0X NAD 0.002395 0.41343 4.73373
52 1PZG A3D 0.001322 0.41673 4.83384
53 1D1T NAD 0.00006604 0.45633 5.02959
54 3NJ4 NAD 0.00816 0.4274 5.02959
55 3NJ4 AFX 0.008213 0.42728 5.02959
56 3CIF NAD 0.0007772 0.409 5.02959
57 1E5Q NDP 0.0008175 0.4092 5.32544
58 2GZ3 NAP 0.00006059 0.4795 5.6213
59 1PL6 572 0.001393 0.40847 5.6213
60 1X7D ORN 0.002098 0.4093 6
61 2VHW NAI 0.0006369 0.42724 6.21302
62 2B4R NAD 0.001069 0.40973 6.50888
63 2AE2 NAP 0.003059 0.40643 6.53846
64 2AE2 PTO 0.003059 0.40643 6.53846
65 3RJ5 NAD 0.002516 0.40748 6.69291
66 1XSE NDP 0.00384 0.40273 6.77966
67 4KP7 1UQ 0.0006194 0.43568 6.80473
68 4KP7 NAP 0.001005 0.43163 6.80473
69 5L4S NAP 0.003504 0.40104 6.80473
70 5L4S 6KX 0.003504 0.40104 6.80473
71 2HK9 NAP 0.0007857 0.40278 6.90909
72 3OID NDP 0.002408 0.40232 6.97674
73 1PR9 NAP 0.002437 0.40213 7.37705
74 3D3W NAP 0.002441 0.40211 7.37705
75 4OOE FOM 0.006634 0.41647 7.42574
76 4OOE NDP 0.006634 0.41647 7.42574
77 4J7U YTZ 0.00263 0.41092 7.63889
78 4J7U NAP 0.00263 0.41092 7.63889
79 5MSO NAP 0.0008636 0.40011 7.69231
80 1ORR NAD 0.002638 0.40088 7.98817
81 2DT5 NAD 0.0007177 0.41078 8.53081
82 2C29 NAP 0.003594 0.40675 8.60534
83 4K28 NAD 0.0004272 0.40733 8.92193
84 4TQG NDP 0.0008751 0.40649 8.97833
85 3QV1 NAD 0.0003039 0.41143 9.7561
86 4XYB NDP 0.0009792 0.41785 10.6509
87 2I3G NAP 0.0008703 0.41292 13.0682
88 1CDO NAD 0.00004209 0.44792 14.2012
89 4W6Z 8ID 0.001081 0.4498 15.0888
90 1P0F NAP 0.000006079 0.49325 15.3846
91 2DM6 IMN 0.000001318 0.53097 18.6186
92 2DM6 NAP 0.000001952 0.52307 18.6186
93 3WLE NAD 0.000001115 0.52884 19.0616
94 4GKV NAD 0.000004867 0.50202 19.2308
95 1YQD NAP 0.00001815 0.47954 19.2308
96 3TWO NDP 0.00001639 0.48431 19.5266
97 5FI3 NAP 0.000101 0.44458 19.8225
98 1U1I NAD 0.002687 0.40182 19.8225
99 2FZW NAD 0.0002822 0.44861 21.7158
100 4B7X NAP 0.000007925 0.49263 22.619
101 4WAS NAP 0.0000365 0.47301 24.5562
102 1N9G NAP 0.000005973 0.46967 24.5562
103 4WAS COO 0.0006661 0.42652 24.5562
104 3B6Z CO7 0.0005156 0.42396 24.5562
105 1U3U NAD 0.00008216 0.46772 25.4438
106 1U3U BNF 0.00008216 0.46772 25.4438
107 1LLU NAD 0.000003204 0.50865 26.3314
108 2JHF NAD 0.0006197 0.48043 26.6272
109 1KEV NDP 0.00011 0.45254 26.9231
110 1YKF NAP 0.0003311 0.42565 26.9231
111 2ZB3 NDP 0.00757 0.40685 26.9231
112 2ZB4 5OP 0.00000893 0.49853 27.5148
113 2ZB4 NAP 0.000008147 0.49853 27.5148
114 1H2B NAJ 0.005095 0.41881 27.8107
115 3JV7 NAD 0.0000008185 0.51706 31.0651
116 4RQU NAD 0.00005698 0.44837 31.9527
117 1R37 NAD 0.001304 0.44401 34.3195
118 3JYN NDP 0.002001 0.43521 35.6923
119 1YB5 NAP 0.003033 0.42914 36.0947
120 3QWB NDP 0.0000002466 0.5388 36.5269
121 4A0S NAP 0.0000000184 0.57831 36.6864
122 1E3I CXF 0.00006398 0.46402 37.8698
123 3GFB NAD 0.0007477 0.40663 37.8698
124 2DFV NAD 0.0001056 0.43491 40.5325
125 4RVU NDP 0.0000004381 0.54022 40.9639
126 4JBI NDP 0.000007978 0.46514 42.3077
127 2J8Z NAP 0.004393 0.41625 48.5207
Pocket No.: 2; Query (leader) PDB : 5DOZ; Ligand: NDP; Similar sites found: 47
This union binding pocket(no: 2) in the query (biounit: 5doz.bio3) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3A06 FOM 0.002959 0.40983 1.47929
2 3A06 NDP 0.002638 0.4094 1.47929
3 1HYH NAD 0.001832 0.41158 1.61812
4 1RKX NAD 0.003069 0.40309 2.07101
5 4XB2 NDP 0.0005116 0.41158 2.08955
6 4XB2 HSE 0.001986 0.41158 2.08955
7 1ZEM NAD 0.001855 0.40121 2.29008
8 1NYT NAP 0.001632 0.4007 2.58303
9 3I6I NDP 0.002916 0.41231 2.66272
10 1BXK NAD 0.002662 0.40108 2.66272
11 2DC1 NAD 0.001841 0.4038 2.9661
12 1XKQ NDP 0.003323 0.40433 3.21429
13 1OC2 NAD 0.009671 0.40547 3.5503
14 1OC2 TDX 0.009671 0.40547 3.5503
15 2BD0 NAP 0.00343 0.40255 3.68852
16 1XG5 NAP 0.002122 0.40916 3.84615
17 3LU1 NAD 0.002277 0.40801 3.84615
18 2JAH NDP 0.00292 0.40391 4.04858
19 2Q1W NAD 0.002776 0.40732 4.14201
20 1JAY NAP 0.0004284 0.40746 4.24528
21 1HDO NAP 0.001664 0.41707 4.36893
22 1GQ2 NAP 0.002793 0.40085 4.73373
23 1KEW NAD 0.008074 0.40569 5.02959
24 5UAV NDP 0.003742 0.40357 5.2795
25 5UAV TFB 0.004013 0.40357 5.2795
26 1RM0 D6P 0.03918 0.40099 5.32544
27 5KKA 6V0 0.002115 0.41054 5.44872
28 1PL6 NAD 0.0003106 0.41094 5.6213
29 1EZ4 NAD 0.001327 0.40729 5.66038
30 1UWK URO 0.002664 0.42085 6.21302
31 1UWK NAD 0.002664 0.42085 6.21302
32 4ZVV NAD 0.007668 0.41173 6.3253
33 4ZVV GN0 0.007668 0.41173 6.3253
34 3VPH OXM 0.004658 0.40108 6.45161
35 2VYN NAD 0.001875 0.40678 7.18563
36 4J4H 1J1 0.006008 0.4076 7.72201
37 4J4H NAI 0.006008 0.4076 7.72201
38 4JK3 NAD 0.001451 0.40521 7.72201
39 2V6G NAP 0.002721 0.40507 9.1716
40 1LDN NAD 0.002451 0.4068 9.49367
41 4EUE NAI 0.003113 0.40416 11.5385
42 4ZGS NAD 0.0007296 0.40899 13.9053
43 5H81 NAP 0.000645 0.40354 14.1388
44 2CVQ NDP 0.002689 0.40115 15.2905
45 2EV9 NAP 0.001691 0.41424 19.7719
46 2EV9 SKM 0.001691 0.41424 19.7719
47 5THQ NDP 0.002805 0.40323 29.7794
Pocket No.: 3; Query (leader) PDB : 5DOZ; Ligand: NDP; Similar sites found: 5
This union binding pocket(no: 3) in the query (biounit: 5doz.bio2) has 31 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4BVA T3 0.004003 0.40694 2.68657
2 3CIF G3H 0.004006 0.4036 5.02959
3 1X7D NAD 0.00231 0.40426 6
4 2B4R AES 0.002639 0.40423 6.50888
5 1NVM NAD 0.003641 0.40028 6.80473
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