Receptor
PDB id Resolution Class Description Source Keywords
4HA9 2.35 Å EC: 1.1.1.302 STRUCTURAL INSIGHTS INTO THE REDUCTION MECHANISM OF SACCHARO CEREVISIA RIBOFLAVIN BIOSYNTHESIS REDUCTASE RIB7 SACCHAROMYCES CEREVISIAE REDUCTASE NADPH BINDING OXIDOREDUCTASE
Ref.: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO SACCHAROMYC CEREVISIAE RIBOFLAVIN BIOSYNTHESIS REDUCTASE RIB7. PLOS ONE V. 8 61249 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NDP A:301;
Valid;
none;
Ka = 15000 M^-1
745.421 C21 H30 N7 O17 P3 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4HA9 2.35 Å EC: 1.1.1.302 STRUCTURAL INSIGHTS INTO THE REDUCTION MECHANISM OF SACCHARO CEREVISIA RIBOFLAVIN BIOSYNTHESIS REDUCTASE RIB7 SACCHAROMYCES CEREVISIAE REDUCTASE NADPH BINDING OXIDOREDUCTASE
Ref.: STRUCTURAL AND FUNCTIONAL INSIGHTS INTO SACCHAROMYC CEREVISIAE RIBOFLAVIN BIOSYNTHESIS REDUCTASE RIB7. PLOS ONE V. 8 61249 2013
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4HA9 Ka = 15000 M^-1 NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4HA9 Ka = 15000 M^-1 NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4HA9 Ka = 15000 M^-1 NDP C21 H30 N7 O17 P3 c1nc(c2c(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 : 4HA9; Ligand: NDP; Similar sites found: 87
This union binding pocket(no: 1) in the query (biounit: 4ha9.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3DFR NDP 0.000000338 0.54548 None
2 1FWV SGA MAG FUC 0.007439 0.44295 None
3 1R6N 434 0.02812 0.40752 None
4 2WOR 2AN 0.02729 0.40686 None
5 1YNS HPO 0.008165 0.4342 2.00803
6 2NW9 FT6 0.02716 0.40602 2.00803
7 2F5X ASP 0.02756 0.40518 2.00803
8 2VVG ADP 0.03041 0.40394 2.00803
9 3FIU POP 0.0349 0.40269 2.00803
10 5HWK BEZ 0.02168 0.4064 2.40964
11 2FZH DH1 0.0000008554 0.43985 2.42718
12 3RG9 NDP 0.00000008358 0.4981 2.5
13 3RG9 WRA 0.0000001114 0.47729 2.5
14 3NOJ PYR 0.01777 0.40279 2.52101
15 3TW1 AHN 0.009203 0.42977 2.53165
16 5E5U MLI 0.001691 0.46263 2.81124
17 1PVS 7HP 0.03277 0.40302 2.81124
18 2BO4 FLC 0.04396 0.40029 2.81124
19 3B6C SDN 0.004157 0.44584 2.99145
20 1JUV NDP 0.0002743 0.4305 3.10881
21 4XFR CIT 0.008289 0.44058 3.21285
22 2IYF UDP 0.00547 0.43467 3.21285
23 3KJS NAP 0.00000003579 0.55261 3.61446
24 4EIL NDP 0.0000002093 0.5367 3.61446
25 3KJS DQ1 0.0000001129 0.46552 3.61446
26 2AWN ADP 0.0194 0.41082 3.61446
27 5O4F 8VE 0.01271 0.40425 3.61446
28 2XT3 ADP 0.0333 0.40281 3.61446
29 4JWK CTN 0.02264 0.40369 3.62694
30 4WBD CIT 0.01611 0.42351 4.01606
31 1KC7 PPR 0.026 0.40533 4.01606
32 2IYA UDP 0.01258 0.40446 4.01606
33 3HGM ATP 0.00494 0.40544 4.08163
34 1U72 NDP 0.000000971 0.60166 4.30108
35 1U70 NDP 0.0000007909 0.59644 4.30108
36 1U70 MTX 0.0000007909 0.43408 4.30108
37 1U72 MTX 0.000000971 0.40818 4.30108
38 4G05 JZ3 0.00795 0.41873 4.41767
39 3LRE ADP 0.0268 0.40062 4.41767
40 3EYK EYK 0.01127 0.4453 4.65116
41 3NRR NAP 0.000000186 0.45361 4.81928
42 3NRR D16 0.0000001716 0.43656 4.81928
43 1MJH ATP 0.003529 0.41158 4.93827
44 4KM2 ATR 0.0000007999 0.46136 5.02793
45 4KM2 TOP 0.0000008454 0.45598 5.02793
46 5FJJ MAN 0.01618 0.45235 5.22088
47 4A4Z ANP 0.02182 0.40039 5.22088
48 1MFI FHC 0.02844 0.4046 5.26316
49 2ACV UDP 0.01344 0.40311 5.62249
50 3W6X HZP 0.01132 0.41445 5.67686
51 3EEL 53T 0.0000001109 0.46609 5.72687
52 1DR1 NAP 0.000001759 0.45411 5.82011
53 1DR1 HBI 0.000001759 0.45411 5.82011
54 2BL9 NDP 0.0000000098 0.51637 5.88235
55 2BL9 CP6 0.0000000098 0.51637 5.88235
56 4A9C B5F 0.02036 0.41272 6.4257
57 3JUC PCA 0.008238 0.42791 6.53595
58 3VY6 BGC BGC 0.01321 0.42794 7.0922
59 1Q8O MAN MMA 0.0214 0.41014 7.22892
60 4OR7 NAP 0.00000003707 0.56245 7.27273
61 2W9S NDP 0.00000006685 0.55981 7.45342
62 5TME UDP 0.00765 0.42282 7.63052
63 1D1G NDP 0.0000001284 0.57016 7.7381
64 4PU6 ASP 0.0235 0.40686 8.39695
65 1NLM UD1 0.008293 0.40566 8.51648
66 2CIG 1DG 0.0000006442 0.43804 8.80503
67 4LAE NAP 0.0000001309 0.42668 8.98204
68 4LAE 1VM 0.0000001309 0.42668 8.98204
69 3IX9 NDP 0.00000009355 0.55549 9.63855
70 3TDC 0EU 0.004884 0.45309 10.0402
71 1NXJ TLA 0.01486 0.41977 10.0402
72 1OYY AGS 0.01988 0.4024 10.0402
73 2I5F 5IP 0.02219 0.40373 10.0917
74 1AOE NDP 0.0000001872 0.46429 10.4167
75 1AOE GW3 0.0000001872 0.46429 10.4167
76 5JCM NAD 0.02043 0.41293 10.4418
77 5JCM ISD 0.0221 0.41132 10.4418
78 5JCM FAD 0.02146 0.41132 10.4418
79 1J3I NDP 0.00000006802 0.47743 10.8434
80 1J3I WRA 0.00000007433 0.47122 10.8434
81 4DP3 MMV 0.0000001116 0.44826 10.8434
82 4DP3 NDP 0.0000001116 0.44826 10.8434
83 5DXV NAP 0.00000166 0.54513 12.1795
84 4M7V NAP 0.00000004825 0.53375 12.5714
85 4M7V RAR 0.0000001257 0.45336 12.5714
86 2J5V PCA 0.004257 0.4488 13.253
87 3IA4 NDP 0.00000001665 0.54768 23.4568
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