FAIRMol

MK216

Pose ID 2958 Compound 534 Pose 248

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T05
L. major PTR1 L. major
Ligand MK216
PDB7PXX↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
40.0 kcal/mol
Protein clashes
4
Internal clashes
1
Native overlap
contact recall 0.47, Jaccard 0.40, H-bond role recall 0.33
Burial
78%
Hydrophobic fit
85%
Reason: no major geometry red flags detected
4 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.907 kcal/mol/HA) ✓ Good fit quality (FQ -8.75) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Very high strain energy (40.0 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (13)
Score
-27.214
kcal/mol
LE
-0.907
kcal/mol/HA
Fit Quality
-8.75
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Strain ΔE
40.0 kcal/mol
SASA buried
78%
Lipo contact
85% BSA apolar/total
SASA unbound
662 Ų
Apolar buried
438 Ų

Interaction summary

HB 11 HY 12 PI 2 CLASH 1

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank1.057Score-27.214
Inter norm-1.059Intra norm0.151
Top1000noExcludedno
Contacts11H-bonds11
Artifact reasongeometry warning; 13 clashes; 4 protein contact clashes; 1 severe cofactor-context clash; high strain Δ 40.0
Residues
ARG17 LEU18 LEU229 LYS16 NDP302 PHE113 SER111 SER112 SER227 TYR194 VAL230

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameligandContacts17
PoseOpen native poseHB0
IFP residues
ARG17 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap8Native recall0.47
Jaccard0.40RMSD-
HB strict3Strict recall0.43
HB same residue+role2HB role recall0.33
HB same residue3HB residue recall0.60

Protein summary

274 residues
Protein targetT05Atoms4108
Residues274Chains2
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
263 1.0267699428225585 -1.16463 -31.7677 11 13 0 0.00 0.00 - no Open
248 1.0565759821753493 -1.05865 -27.2137 11 11 8 0.47 0.33 - no Current
275 1.158072578337196 -0.79049 -20.4723 4 16 0 0.00 0.00 - no Open
326 1.522628122716502 -0.968338 -25.9969 6 13 0 0.00 0.00 - no Open
244 1.708744967754064 -0.825708 -20.6159 5 19 0 0.00 0.00 - no Open
257 1.8345663825114074 -0.798505 -19.855 3 19 0 0.00 0.00 - no Open
309 1.905113599274035 -0.859805 -26.3343 3 12 0 0.00 0.00 - no Open
209 2.4824832058938013 -1.05337 -29.243 13 18 0 0.00 0.00 - no Open
204 2.663282674439042 -1.13906 -30.5138 11 18 0 0.00 0.00 - no Open
270 2.7066301048038337 -0.90359 -23.3047 8 16 0 0.00 0.00 - no Open
335 3.062936325722447 -0.858552 -27.4791 7 19 0 0.00 0.00 - no Open
224 3.0864929722424383 -0.941482 -26.4284 4 18 0 0.00 0.00 - no Open
308 3.1241016565923485 -1.04343 -27.852 6 10 0 0.00 0.00 - no Open
210 3.431812628247348 -1.01323 -26.2551 13 17 0 0.00 0.00 - no Open
200 4.283886601626247 -0.994469 -27.0487 13 17 0 0.00 0.00 - no Open
213 4.298392329825456 -0.999515 -28.3054 11 16 0 0.00 0.00 - no Open
307 4.451695165235262 -0.776336 -19.1475 5 13 0 0.00 0.00 - no Open
249 5.404412263953654 -0.824137 -19.6852 7 12 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -27.214kcal/mol
Ligand efficiency (LE) -0.9071kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.750
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.80
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 65.46kcal/mol
Minimised FF energy 25.48kcal/mol

SASA & burial

✓ computed
SASA (unbound) 662.2Ų
Total solvent-accessible surface area of free ligand
BSA total 517.0Ų
Buried surface area upon binding
BSA apolar 438.4Ų
Hydrophobic contacts buried
BSA polar 78.6Ų
Polar contacts buried
Fraction buried 78.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1719.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1038.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)