FAIRMol

MK213

Pose ID 9115 Compound 534 Pose 307

DB SELECTIONDocking 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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand MK213
PDB1NJJ↗

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 high Native strong SASA done
Strain ΔE
21.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.60, Jaccard 0.47, H-bond role recall 0.20
Burial
61%
Hydrophobic fit
80%
Reason: no major geometry red flags detected
2 protein-contact clashes 74% of hydrophobic surface is solvent-exposed (17/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.638 kcal/mol/HA) ✓ Good fit quality (FQ -6.16) ✓ Good H-bonds (5 bonds) ✓ Good burial (61% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ High strain energy (21.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-19.148
kcal/mol
LE
-0.638
kcal/mol/HA
Fit Quality
-6.16
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Strain ΔE
21.4 kcal/mol
SASA buried
61%
Lipo contact
80% BSA apolar/total
SASA unbound
675 Ų
Apolar buried
329 Ų

Interaction summary

HB 5 HY 2 PI 0 CLASH 2 ⚠ Exposure 73%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
74% of hydrophobic surface is solvent-exposed (17/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 23 Buried (contacted) 6 Exposed 17 LogP 3.8 H-bonds 5
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (2/5 atoms exposed)aliphatic chain/group (6 atoms exposed)
Final rank4.452Score-19.148
Inter norm-0.776Intra norm0.138
Top1000noExcludedno
Contacts13H-bonds5
Artifact reasongeometry warning; 12 clashes; 3 protein clashes; moderate strain Δ 21.4
Residues
ARG242 ARG337 ASP243 ASP385 GLU384 LEU339 LEU382 MET386 PHE383 PRO338 SER282 THR241 VAL336

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

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:ORX602

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap9Native recall0.60
Jaccard0.47RMSD-
HB strict0Strict recall0.00
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

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 0 0.00 0.00 - no Open
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 9 0.60 0.20 - no Current
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 -19.148kcal/mol
Ligand efficiency (LE) -0.6382kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.157
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) 21.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 57.08kcal/mol
Minimised FF energy 35.70kcal/mol

SASA & burial

✓ computed
SASA (unbound) 674.7Ų
Total solvent-accessible surface area of free ligand
BSA total 411.5Ų
Buried surface area upon binding
BSA apolar 329.2Ų
Hydrophobic contacts buried
BSA polar 82.3Ų
Polar contacts buried
Fraction buried 61.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2526.2Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1392.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)