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Receptor
PDB id Resolution Class Description Source Keywords
1V9N 2.1 Å EC: 1.1.1.37 STRUCTURE OF MALATE DEHYDROGENASE FROM PYROCOCCUS HORIKOSHII PYROCOCCUS HORIKOSHII DEHYDROGENASE RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATISTRUCTURAL GENOMICS OXIDOREDUCTASE
Ref.: STRUCTURE OF MALATE DEHYDROGENASE FROM PYROCOCCUS H OT3 TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:403;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NDP A:401;
Valid;
none;
submit data
745.421 C21 H30 N7 O17 P3 c1nc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1V9N 2.1 Å EC: 1.1.1.37 STRUCTURE OF MALATE DEHYDROGENASE FROM PYROCOCCUS HORIKOSHII PYROCOCCUS HORIKOSHII DEHYDROGENASE RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATISTRUCTURAL GENOMICS OXIDOREDUCTASE
Ref.: STRUCTURE OF MALATE DEHYDROGENASE FROM PYROCOCCUS H OT3 TO BE PUBLISHED
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 1V9N - 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 8 families.
1 1V9N - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1VBI - NAD C21 H27 N7 O14 P2 c1cc(c[n+]....
2 1V9N - NDP C21 H30 N7 O17 P3 c1nc(c2c(n....
3 4FJU - GLV C2 H2 O3 C(=O)C(=O)....
4 4H8A - NAI C21 H29 N7 O14 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NDP; Similar ligands found: 172
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 1DG 0.68 1
8 DG1 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 80F 0.537879 0.914634
23 2AM 0.529412 0.87013
24 6V0 0.519685 0.974026
25 NAP 0.514493 0.922078
26 7L1 0.507143 0.763441
27 EAD 0.507143 0.949367
28 A2D 0.504673 0.921053
29 TXE 0.503876 0.935897
30 NA0 0.496454 0.910256
31 TXD 0.496124 0.911392
32 SAP 0.495575 0.875
33 AGS 0.495575 0.875
34 P1H 0.493056 0.925926
35 CO7 0.489796 0.791209
36 TAP 0.489362 0.864198
37 PAP 0.482456 0.907895
38 BA3 0.481818 0.921053
39 NAJ PZO 0.478261 0.924051
40 ATP 0.477876 0.921053
41 HEJ 0.477876 0.921053
42 B4P 0.477477 0.921053
43 AP5 0.477477 0.921053
44 ADP 0.477477 0.921053
45 OAD 0.47541 0.897436
46 AR6 0.473684 0.896104
47 AQP 0.473684 0.921053
48 5FA 0.473684 0.921053
49 APR 0.473684 0.896104
50 AN2 0.473214 0.909091
51 3OD 0.467742 0.897436
52 50T 0.464912 0.884615
53 NAJ PYZ 0.464789 0.879518
54 9X8 0.463415 0.851852
55 PO4 PO4 A A A A PO4 0.463415 0.857143
56 V3L 0.461538 0.896104
57 2A5 0.46087 0.85
58 AT4 0.460177 0.886076
59 A1R 0.459016 0.841463
60 4AD 0.459016 0.875
61 ADQ 0.459016 0.897436
62 OVE 0.458716 0.8375
63 OMR 0.458647 0.813953
64 PPS 0.457627 0.811765
65 AD9 0.456897 0.897436
66 CA0 0.45614 0.897436
67 M33 0.45614 0.884615
68 ADJ 0.455882 0.879518
69 A3P 0.455357 0.894737
70 ACP 0.452174 0.897436
71 ENP 0.451613 0.85
72 UP5 0.451128 0.948052
73 SRP 0.45 0.8625
74 ANP 0.449153 0.897436
75 ACQ 0.449153 0.897436
76 PRX 0.448276 0.82716
77 A3R 0.447154 0.841463
78 5AL 0.445378 0.884615
79 7D4 0.443478 0.8375
80 ADX 0.443478 0.811765
81 6YZ 0.438017 0.897436
82 A 0.436364 0.894737
83 AMP 0.436364 0.894737
84 4TC 0.433824 0.924051
85 7D3 0.433628 0.8375
86 DCA 0.433566 0.788889
87 ETB 0.433566 0.797753
88 BIS 0.433071 0.864198
89 1ZZ 0.433071 0.802326
90 00A 0.432 0.864198
91 ATF 0.429752 0.886076
92 DQV 0.428571 0.934211
93 0T1 0.427586 0.788889
94 5SV 0.427419 0.788235
95 8QN 0.427419 0.884615
96 3AM 0.427273 0.857143
97 N01 0.426573 0.884615
98 PR8 0.425197 0.811765
99 LAD 0.425197 0.821429
100 WAQ 0.425197 0.841463
101 DTP 0.425 0.8375
102 AMO 0.424 0.886076
103 PAJ 0.424 0.843373
104 APC 0.423729 0.886076
105 UPA 0.423358 0.935897
106 48N 0.422222 0.853659
107 FYA 0.421875 0.860759
108 PTJ 0.421875 0.853659
109 CNA 0.421429 0.910256
110 PUA 0.42069 0.9125
111 DND 0.419118 0.910256
112 NXX 0.419118 0.910256
113 AV2 0.418033 0.848101
114 COA 0.417808 0.788889
115 3UK 0.417323 0.897436
116 OOB 0.416 0.909091
117 IVC 0.415584 0.78022
118 DAT 0.415254 0.8375
119 NDO 0.414966 0.897436
120 139 0.414286 0.901235
121 B5V 0.414062 0.886076
122 T99 0.413223 0.886076
123 TAT 0.413223 0.886076
124 3AT 0.413223 0.896104
125 YLB 0.413043 0.784091
126 62F 0.4125 0.823529
127 ABM 0.412281 0.848101
128 B5M 0.412214 0.875
129 YAP 0.412214 0.875
130 YLP 0.411765 0.784091
131 NB8 0.410853 0.853659
132 ME8 0.410853 0.802326
133 SON 0.410256 0.886076
134 DLL 0.409449 0.909091
135 AHX 0.409449 0.853659
136 CAO 0.409396 0.763441
137 30N 0.409396 0.72449
138 AMX 0.409396 0.797753
139 COS 0.409396 0.771739
140 7D5 0.409091 0.8125
141 4UW 0.408759 0.9125
142 F2R 0.408451 0.825581
143 APX 0.407692 0.841463
144 SRA 0.40708 0.85
145 CMX 0.406667 0.788889
146 SCO 0.406667 0.788889
147 TYM 0.405797 0.886076
148 COD 0.405594 0.777778
149 CA6 0.405229 0.70297
150 OXK 0.405229 0.771739
151 AP2 0.405172 0.886076
152 A12 0.405172 0.886076
153 9SN 0.40458 0.853659
154 LAQ 0.404412 0.802326
155 T5A 0.404255 0.914634
156 FAM 0.403974 0.771739
157 ACO 0.403974 0.763441
158 FCX 0.403974 0.763441
159 VO4 ADP 0.403226 0.860759
160 ADP VO4 0.403226 0.860759
161 YLC 0.402878 0.823529
162 1VU 0.402597 0.763441
163 B5Y 0.401515 0.875
164 FA5 0.401515 0.886076
165 HAX 0.401316 0.771739
166 AR6 AR6 0.4 0.871795
167 CAJ 0.4 0.771739
168 AFH 0.4 0.843373
169 APU 0.4 0.923077
170 A U 0.4 0.898734
171 TXA 0.4 0.886076
172 4UU 0.4 0.948052
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1V9N; Ligand: NDP; Similar sites found with APoc: 63
This union binding pocket(no: 1) in the query (biounit: 1v9n.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
1 4CQK PIO None
2 1GOJ ADP 1.69014
3 5X30 HCS 1.94444
4 5WP4 PC 1.94444
5 1QDS PGA 1.99203
6 4PPF FLC 2
7 4QHP 32R 2.22222
8 5NC1 NAG 2.22222
9 5NM7 GLY 2.25564
10 2Y91 98J 2.26415
11 3THR C2F 2.38908
12 5YLF BGC 2.39521
13 2OI2 DP6 2.39726
14 3BMN AX3 2.43056
15 5H4S RAM 2.46479
16 3MBC NAP 2.5
17 4NZ6 DGL 2.55591
18 5URY PAM 2.73973
19 2J5V PCA 2.77778
20 1A5V Y3 3.16456
21 1YXM ADE 3.30033
22 6F5W KG1 3.33333
23 2UVO NDG 3.50877
24 2UVO NAG 3.50877
25 2DT9 THR 3.59281
26 2Z49 AMG 3.61111
27 2Z48 NGA 3.61111
28 5W75 SUC 3.88889
29 1RRC ADP 3.98671
30 5A96 GTP 4.01606
31 5E5U MLI 4.0201
32 5GVR LMR 4.2735
33 1Q19 SSC 4.44444
34 2CXG GLC GLC 4.44444
35 1B4N GUA 4.44444
36 4RF7 ARG 4.72222
37 5NXX 3Q7 4.85075
38 5C9P FUC 5
39 3AB4 THR 5.05618
40 2DTJ THR 5.05618
41 3LRE ADP 5.07042
42 3DUV KDO 5.34351
43 1VB3 KPA 5.83333
44 3GUZ PAF 6.25
45 1TD2 PXL 6.27178
46 2VVG ADP 6.57143
47 2AWN ADP 6.66667
48 5HV0 AKG 6.91244
49 2O66 FLC 7.40741
50 4YJ1 ADP 7.5
51 5L3S G 7.77027
52 1GXU 2HP 8.79121
53 4Y4V DAL 9.14454
54 2WDQ TEO 10.8527
55 1XPJ TLA 11.1111
56 3A4M ADP 11.1538
57 1MQ0 BRD 11.4286
58 3K1X DBX 13.0769
59 2G30 ALA ALA PHE 14.3411
60 1S20 NAD 41.7647
61 1Z2I NAD 46.1111
62 2CWH NDP 47.2303
63 2CWH PYC 47.2303
Pocket No.: 2; Query (leader) PDB : 1V9N; Ligand: NDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1v9n.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
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