Receptor
PDB id Resolution Class Description Source Keywords
4UOG 2.3 Å EC: 2.7.4.6 CRYSTALLOGRAPHIC STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM LITOPENAEUS VANNAMEI COMPLEXED WITH DCDP LITOPENAEUS VANNAMEI TRANSFERASE BINARY COMPLEX DCDP PYRIMIDINE BINDING SITEDESOXYNUCLEOTIDE
Ref.: STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM PAC SHRIMP (LITOPENAEUS VANNAMEI) IN BINARY COMPLEXES W PURINE AND PYRIMIDINE NUCLEOSIDE DIPHOSPHATES ACTA CRYSTALLOGR.,SECT.F V. 79 1150 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
YYY A:1152;
C:1152;
B:1152;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
387.177 C9 H15 N3 O10 P2 C1[C@...
MG A:1153;
B:1153;
C:1153;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4UOH 2.01 Å EC: 2.7.4.6 CRYSTALLOGRAPHIC STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM LITOPENAEUS VANNAMEI COMPLEXED WITH ADP LITOPENAEUS VANNAMEI TRANSFERASE BINARY COMPLEX ADP PURINE WHITE-SHRIMP BINSITE NUCLEOTIDE
Ref.: STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM PAC SHRIMP (LITOPENAEUS VANNAMEI) IN BINARY COMPLEXES W PURINE AND PYRIMIDINE NUCLEOSIDE DIPHOSPHATES ACTA CRYSTALLOGR.,SECT.F V. 79 1150 2014
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
2 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
70% Homology Family (25)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1F6T - TBD C10 H19 B N2 O10 P2 [BH3-][P@@....
2 1NDP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3FKB - TNM C9 H15 N5 O7 P2 C[C@H](Cn1....
4 1KDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1LWX - AZD C10 H15 N5 O10 P2 CC1=CN(C(=....
6 1NDC - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
7 2BEF - BEF ADP n/a n/a
8 1F3F Kd = 21.3 uM D4T C10 H15 N2 O13 P3 CC1=CN(C(=....
9 4CP5 Kd = 452 uM EOI C9 H16 N5 O9 P3 S C[C@H](Cn1....
10 1B4S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1S5Z - SON C12 H16 N5 O8 P c1nc(c2c(n....
12 1MN7 - ABT C10 H17 B N5 O12 P3 B=P(O)(OC[....
13 3NGU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
14 1WKL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
15 1ZS6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
17 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
18 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
19 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
20 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
21 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
22 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
23 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
25 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50% Homology Family (51)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1F6T - TBD C10 H19 B N2 O10 P2 [BH3-][P@@....
2 1NDP - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 3FKB - TNM C9 H15 N5 O7 P2 C[C@H](Cn1....
4 1KDN - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
5 1LWX - AZD C10 H15 N5 O10 P2 CC1=CN(C(=....
6 1NDC - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
7 2BEF - BEF ADP n/a n/a
8 1F3F Kd = 21.3 uM D4T C10 H15 N2 O13 P3 CC1=CN(C(=....
9 4CP5 Kd = 452 uM EOI C9 H16 N5 O9 P3 S C[C@H](Cn1....
10 1B4S - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
11 1S5Z - SON C12 H16 N5 O8 P c1nc(c2c(n....
12 1MN7 - ABT C10 H17 B N5 O12 P3 B=P(O)(OC[....
13 3EVO - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
14 3ELH - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
15 3GP9 - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
16 3EJM - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
17 3FBB - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
18 3EMT - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
19 3FCV - DUD C9 H14 N2 O11 P2 C1[C@@H]([....
20 3EIC - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
21 3EVM - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
22 3B6B - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
23 3FCW - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
24 2B8Q - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
25 3DKD - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
26 3DDI - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
27 3FBE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
28 3ETM - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
29 3GPA - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
30 3ENA - DGI C10 H15 N5 O10 P2 c1nc2c(n1[....
31 3EM1 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
32 3EE3 - CDP MG n/a n/a
33 3NGU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
34 3Q86 - GTP MG n/a n/a
35 3Q8U - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
36 3Q8V - UDP C9 H14 N2 O12 P2 C1=CN(C(=O....
37 1WKL - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
38 1ZS6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
39 4UOG - YYY C9 H15 N3 O10 P2 C1[C@@H]([....
40 4UOH - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
41 2AZ3 - CDP C9 H15 N3 O11 P2 C1=CN(C(=O....
42 1NHK - CMP C10 H12 N5 O6 P c1nc(c2c(n....
43 1NLK - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 1BE4 - PCG C10 H12 N5 O7 P c1nc2c(n1[....
45 3BBB - DG C10 H14 N5 O7 P c1nc2c(n1[....
46 1NUE - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
47 1BHN - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
48 2HVD - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
49 1UCN Kd = 6 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
50 3BBF - GDP C10 H15 N5 O11 P2 c1nc2c(n1[....
51 2HVE - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YYY; Similar ligands found: 50
No: Ligand ECFP6 Tc MDL keys Tc
1 YYY 1 1
2 DCP 0.884058 1
3 DCM 0.80597 0.985714
4 DC 0.80597 0.985714
5 DCP MG 0.692308 0.905405
6 DCZ 0.641791 0.847222
7 LDC 0.641791 0.847222
8 DUD 0.589744 0.929577
9 CDP 0.582278 0.90411
10 GCQ 0.554217 0.891892
11 TYD 0.536585 0.891892
12 CTP 0.52381 0.90411
13 DUT 0.52381 0.929577
14 DOC 0.4875 0.957747
15 CPA 0.485981 0.85
16 8GD 0.483516 0.875
17 6U4 0.478723 0.921053
18 TTP 0.477273 0.891892
19 CGP 0.468468 0.841463
20 7XL 0.466667 0.88
21 8DD 0.457447 0.835443
22 DU 0.451219 0.915493
23 C5P 0.451219 0.890411
24 CAR 0.451219 0.890411
25 C 0.451219 0.890411
26 UMP 0.451219 0.915493
27 CXY 0.44898 0.88
28 CDC 0.447917 0.77381
29 DG DC 0.441667 0.851852
30 C2G 0.43617 0.891892
31 DUP 0.433333 0.90411
32 8DG 0.43299 0.875
33 CDM 0.428571 0.858974
34 DC DG 0.426087 0.819277
35 C5G 0.424242 0.855263
36 C3P 0.421687 0.876712
37 DDN 0.421687 0.915493
38 C2P 0.421687 0.916667
39 CDP MG 0.41573 0.818182
40 UFP 0.411765 0.855263
41 LTT 0.410256 0.77027
42 UC5 0.409091 0.916667
43 DAT 0.408602 0.831169
44 BRU 0.406977 0.855263
45 TMP 0.406977 0.878378
46 DGI 0.40625 0.848101
47 3TC 0.405063 0.76
48 TLO 0.40404 0.844156
49 DUN 0.4 0.90411
50 0FX 0.4 0.835443
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4UOH; Ligand: ADP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4uoh.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4UOH; Ligand: ADP; Similar sites found: 151
This union binding pocket(no: 2) in the query (biounit: 4uoh.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3S9K CIT 0.0003036 0.53153 None
2 2YD6 FLC 0.001454 0.49435 None
3 1UO5 PIH 0.003373 0.45989 None
4 3F81 STT 0.00475 0.43344 None
5 1WTC ACP 0.00248 0.43107 None
6 2ALG DAO 0.001475 0.42703 None
7 1TUV VK3 0.009407 0.41916 None
8 1UO4 PIH 0.02283 0.4077 None
9 2QLX RM4 0.008666 0.40706 None
10 4A3X LAT 0.01874 0.40472 None
11 1G0V NAG 0.00137 0.48458 1.3245
12 3P3N AKG 0.006104 0.40755 1.3245
13 1GPJ CIT 0.006795 0.40557 1.3245
14 2Y0I AKG 0.005786 0.40275 1.3245
15 4EXO PYR 0.003796 0.43014 1.36986
16 1Z42 HBA 0.0007069 0.49789 1.98676
17 1Z44 NPO 0.005058 0.45057 1.98676
18 2VQ5 HBA 0.00245 0.4313 1.98676
19 2FPU HSO 0.005735 0.41499 1.98676
20 1OIK AKG 0.005598 0.40915 1.98676
21 3SBZ MLI 0.01826 0.40526 1.98676
22 3L6R MLI 0.01107 0.40236 1.98676
23 2OFD NGA 0.00655 0.40625 2.11268
24 2WCV FUC 0.001829 0.40349 2.14286
25 3IHB TRS 0.02335 0.44672 2.64901
26 2X2T GAL NGA 0.007762 0.42319 2.64901
27 1II5 GLU 0.003057 0.41409 2.64901
28 3IHB GLU 0.006709 0.41198 2.64901
29 2XRH NIO 0.007613 0.40955 3
30 1NU4 MLA 0.01204 0.43061 3.09278
31 1HFA PIO 0.00001638 0.58477 3.31126
32 4AF5 CIT 0.0006089 0.45003 3.31126
33 4B16 NAG 0.006263 0.4361 3.31126
34 2Q09 DI6 0.0008871 0.42346 3.31126
35 4O8A 2OP 0.009039 0.42 3.31126
36 3SCH TB6 0.004206 0.41442 3.31126
37 1WGC SIA GAL BGC 0.01787 0.41311 3.31126
38 3UDG TMP 0.01439 0.41026 3.31126
39 3BRE C2E 0.005609 0.40911 3.31126
40 1ZZ7 S0H 0.003008 0.40862 3.31126
41 2EB5 OXL 0.006185 0.4073 3.31126
42 1OGD RIP 0.003421 0.40641 3.81679
43 3ZGE ASP 0.002999 0.43484 3.97351
44 1H16 PYR 0.003124 0.43402 3.97351
45 1RYI GOA 0.01557 0.42697 3.97351
46 4K7O EKZ 0.00391 0.42234 3.97351
47 1Y9Q MED 0.004252 0.41422 3.97351
48 3B8I OXL 0.02243 0.4081 3.97351
49 5EQU AKG 0.01143 0.40808 3.97351
50 1R37 ETX 0.006421 0.40661 3.97351
51 2HW1 FRU 0.005244 0.4045 3.97351
52 4F8L GAL 0.002537 0.46643 4.13793
53 3TKA CTN 0.0007513 0.51631 4.63576
54 3WKX FUB 0.0009942 0.441 4.63576
55 1TDF FAD 0.005487 0.43979 4.63576
56 1TDF NAP 0.01299 0.43724 4.63576
57 1NX4 AKG 0.001266 0.42974 4.63576
58 1U5V ATP 0.02665 0.41801 4.63576
59 3CBG FER 0.001243 0.4614 5.29801
60 2ZWS PLM 0.005048 0.45062 5.29801
61 1O9U ADZ 0.002359 0.44804 5.29801
62 4N7U 2JA 0.004376 0.43515 5.29801
63 1I0Z OXM 0.007284 0.42451 5.29801
64 3R51 MMA 0.007331 0.42438 5.29801
65 2XDQ MGX 0.007544 0.42378 5.29801
66 1SOW OXL 0.008081 0.42234 5.29801
67 2BO4 FLC 0.004627 0.41911 5.29801
68 2PYU IMP 0.004014 0.40925 5.29801
69 1YHM AHD 0.004934 0.40558 5.29801
70 4C6F DOR 0.001628 0.40533 5.29801
71 4C6F NCD 0.001628 0.40533 5.29801
72 4RJK PYR 0.01507 0.40253 5.29801
73 1YFZ IMP 0.00597 0.4022 5.29801
74 4COQ SAN 0.009081 0.40021 5.29801
75 1Y2W NAG 0.002612 0.4232 5.6338
76 1BTN I3P 0.004687 0.44829 5.66038
77 3MAG 3MA 0.0009439 0.47744 5.96026
78 4B9E FAH 0.001804 0.43717 5.96026
79 2J0W ASP 0.002823 0.42859 5.96026
80 9LDB OXM 0.0105 0.42477 5.96026
81 1GXS DKA 0.01124 0.40813 5.96026
82 4WBD CIT 0.01189 0.40728 5.96026
83 1XX4 BAM 0.01686 0.40694 5.96026
84 1MZV AMP 0.001904 0.40303 5.96026
85 2VWT PYR 0.0119 0.40096 5.96026
86 4JCA CIT 0.005634 0.43842 5.98802
87 3ICV NAG 0.01068 0.42962 6.62252
88 1RQH PYR 0.003299 0.4256 6.62252
89 1Y7P RIP 0.006273 0.42009 6.62252
90 1Y1A GSH 0.02376 0.41989 6.62252
91 3O03 GCO 0.01279 0.41273 6.62252
92 5YAS FAC 0.00364 0.40279 6.62252
93 2IOY RIP 0.01411 0.40275 6.62252
94 2O66 FLC 0.005596 0.40335 6.66667
95 3QDX A2G GAL 0.001641 0.44687 6.99301
96 3QDT A2G GAL 0.001984 0.44309 6.99301
97 3QDY A2G GAL 0.002817 0.43609 6.99301
98 3QDV NDG 0.002972 0.43502 6.99301
99 3QDW NDG 0.002663 0.4297 6.99301
100 3QDY CBS 0.004161 0.42115 6.99301
101 3QDX CBS 0.005352 0.41632 6.99301
102 3QDW A2G 0.008063 0.4071 6.99301
103 3QDV A2G 0.009223 0.40378 6.99301
104 2FUE M1P 0.002764 0.42216 7.28477
105 4M5P MLA 0.01194 0.42197 7.28477
106 3UBW 6SP 0.0171 0.41785 7.28477
107 1DRJ RIP 0.0137 0.40392 7.28477
108 4FGC PQ0 0.001764 0.42386 7.94702
109 2AEB ABH 0.01947 0.40349 7.94702
110 2B7N NTM 0.006409 0.40093 7.94702
111 1KC7 PPR 0.01201 0.40079 7.94702
112 2BZ1 TAU 0.005658 0.448 8.60927
113 3HZL 6PC 0.004201 0.436 8.60927
114 3BLI PYR 0.004721 0.41873 8.60927
115 1O68 KIV 0.003605 0.40551 8.60927
116 3RF4 FUN 0.004403 0.40208 8.62069
117 1OGZ EQU 0.0006667 0.41136 8.8
118 2XI7 XI7 0.003777 0.45729 9.27152
119 1H8G CHT 0.005485 0.44871 9.47368
120 3VPD BUA 0.008627 0.44377 9.93377
121 3VPD CIT 0.006943 0.43385 9.93377
122 3U1T MLI 0.003344 0.42534 9.93377
123 3I0O SMI 0.001969 0.4219 9.93377
124 1IYE PGU 0.001824 0.44446 10.596
125 1A59 CIT 0.004445 0.41988 10.596
126 1M1B SPV 0.006506 0.40067 10.596
127 1DL7 NCH 0.01734 0.42218 11.0092
128 2BLE 5GP 0.01519 0.42797 11.2583
129 2Q3M MLA 0.01377 0.41119 11.2583
130 3NNF AKG 0.008529 0.40137 11.2583
131 4G1V FAD 0.01567 0.40096 11.2583
132 1JAC AMG 0.02831 0.40295 11.2782
133 1C1L GAL BGC 0.009865 0.40457 12.4088
134 3FPZ AHZ 0.00465 0.46167 12.5828
135 1G8S MET 0.0008379 0.44415 12.5828
136 4RNV HBA 0.006291 0.43848 12.5828
137 1VBH PEP 0.003436 0.41202 12.5828
138 4W6Z ETF 0.01123 0.40843 12.5828
139 1H8P PC 0.003149 0.44202 12.844
140 3GM5 CIT 0.004381 0.41367 13.245
141 1DXY COI 0.01544 0.40879 13.9073
142 2ZJ5 ADP 0.004404 0.40761 13.9073
143 1SS4 GSH 0.0007714 0.50194 14.5695
144 1SS4 CIT 0.02565 0.4408 14.5695
145 3CQ5 PMP 0.003519 0.40065 15.894
146 4CCN OGA 0.001665 0.4315 17.1429
147 2ZE3 AKG 0.005448 0.40382 17.2185
148 3CL5 SIO 0.01018 0.40397 17.8808
149 3ZLM ANP 0.008045 0.40032 19.2053
150 3ZPG 5GP 0.0118 0.41442 19.8675
151 2YIV NBN 0.006045 0.41398 20.5298
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