SMTL ID : 8co0.1

Three dimensional structure of human carbonic anhydrase IX in complex with sulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.92, H.94, E.104, H.117 Ligands: V8O.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.92, A:H.94, A:H.117 ZN.4: 5 residues within 4Å: Chain B: H.92, H.94, E.104, H.117 Ligands: V8O.5 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.92, B:H.94, B:H.117 ZN.7: 5 residues within 4Å: Chain C: H.92, H.94, E.104, H.117 Ligands: V8O.8 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.92, C:H.94, C:H.117 ZN.10: 5 residues within 4Å: Chain D: H.92, H.94, E.104, H.117 Ligands: V8O.11 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.92, D:H.94, D:H.117

4 x V8O: 5-(5-methyl-6-quinolin-5-yl-pyridin-3-yl)thiophene-2-sulfonamide(Non-covalent)

V8O.2: 14 residues within 4Å: Chain A: Q.90, H.92, H.94, E.104, H.117, V.119, V.128, V.140, L.197, T.198, T.199, W.208 Ligands: ZN.1, GOL.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.119, A:V.128, A:V.128, A:L.197 Hydrogen bonds: A:E.104, A:T.198 Water bridges: A:V.128 V8O.5: 14 residues within 4Å: Chain B: H.92, H.94, E.104, H.117, V.119, V.128, L.132, V.140, L.197, T.198, T.199, W.208 Ligands: ZN.4, GOL.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.128, B:L.132, B:L.197 Hydrogen bonds: B:E.104, B:T.198 Water bridges: B:V.128 V8O.8: 14 residues within 4Å: Chain C: L.89, H.92, H.94, E.104, H.117, V.119, V.128, V.140, L.197, T.198, T.199, W.208 Ligands: ZN.7, GOL.9 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.89, C:V.128, C:V.128 Hydrogen bonds: C:T.198, C:T.198 Water bridges: C:Q.90 V8O.11: 13 residues within 4Å: Chain D: H.92, H.94, E.104, H.117, V.119, V.128, L.132, L.197, T.198, T.199, W.208 Ligands: ZN.10, GOL.12 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.132, D:L.197, D:T.199 Hydrogen bonds: D:E.104, D:T.198

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 10 residues within 4Å: Chain A: Y.9, N.64, H.66, S.67, Q.69, Q.90, H.92, H.94, T.199 Ligands: V8O.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.9, A:N.64, A:Q.90 GOL.6: 8 residues within 4Å: Chain B: N.64, H.66, S.67, Q.69, Q.90, H.92, T.199 Ligands: V8O.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.9, B:Y.9, B:N.64, B:Q.69, B:Q.90 Water bridges: B:Q.69, B:Q.69 GOL.9: 7 residues within 4Å: Chain C: N.64, S.67, Q.69, Q.90, H.92, T.199 Ligands: V8O.8 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.64, C:N.64, C:Q.90, C:T.199 Water bridges: C:Y.9, C:Q.69, C:H.94 GOL.12: 8 residues within 4Å: Chain D: N.64, H.66, S.67, Q.69, Q.90, H.92, T.199 Ligands: V8O.11 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.64, D:Q.69, D:Q.90 Water bridges: D:Q.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ivanova, J.N. et al., Atropo/Tropo Flexibility: A Tool for Design and Synthesis of Self-Adaptable Inhibitors of Carbonic Anhydrases and Their Antiproliferative Effect. J.Med.Chem. (2023)

Release Date

2023-12-13

Peptides

Carbonic anhydrase 9: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
E

D
G

Carbonic anhydrase 9

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