FAIRMol

MK220

Pose ID 9122 Compound 167 Pose 314

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 MK220
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
28.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.60, Jaccard 0.47, H-bond role recall 0.20
Burial
64%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
1 protein-contact clashes 100% of hydrophobic surface is solvent-exposed (25/25 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 (-0.635 kcal/mol/HA) ✓ Good fit quality (FQ -6.24) ✓ Strong H-bond network (7 bonds) ✓ Good burial (64% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ High strain energy (28.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-20.315
kcal/mol
LE
-0.635
kcal/mol/HA
Fit Quality
-6.24
FQ (Leeson)
HAC
32
heavy atoms
MW
438
Da
LogP
4.28
cLogP
Strain ΔE
28.9 kcal/mol
SASA buried
64%
Lipo contact
76% BSA apolar/total
SASA unbound
712 Ų
Apolar buried
346 Ų

Interaction summary

HB 7 HY 0 PI 0 CLASH 1 ⚠ Exposure 100%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (25/25 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 25 Buried (contacted) 0 Exposed 25 LogP 4.28 H-bonds 7
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (8 atoms exposed)
Final rank3.716Score-20.315
Inter norm-0.874Intra norm0.239
Top1000noExcludedno
Contacts13H-bonds7
Artifact reasongeometry warning; 12 clashes; 2 protein clashes; moderate strain Δ 28.7
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
No hy · hydrophobic contacts detected for this pose.

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
340 1.3223938073115098 -0.927161 -24.2651 8 16 0 0.00 0.00 - no Open
394 2.014161173473132 -0.775497 -19.6976 10 10 0 0.00 0.00 - no Open
290 2.73482945957276 -0.878682 -21.3656 12 17 0 0.00 0.00 - no Open
249 3.165423711787248 -0.802147 -20.1063 3 19 0 0.00 0.00 - no Open
314 3.7162080227370713 -0.874068 -20.3152 7 13 9 0.60 0.20 - no Current
365 3.9636524130908617 -0.716261 -19.4033 6 14 0 0.00 0.00 - no Open
217 4.166365624759972 -0.935886 -25.7232 10 16 0 0.00 0.00 - no Open
330 4.277927265958028 -0.950834 -24.4595 5 17 0 0.00 0.00 - no Open
321 4.96208626260307 -0.705542 -18.3404 7 11 0 0.00 0.00 - no Open
241 5.4952799348659935 -0.968125 -29.9385 9 25 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 -20.315kcal/mol
Ligand efficiency (LE) -0.6349kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.243
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 437.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.28
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 50.15kcal/mol
Minimised FF energy 21.23kcal/mol

SASA & burial

✓ computed
SASA (unbound) 711.5Ų
Total solvent-accessible surface area of free ligand
BSA total 453.1Ų
Buried surface area upon binding
BSA apolar 346.1Ų
Hydrophobic contacts buried
BSA polar 106.9Ų
Polar contacts buried
Fraction buried 63.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2555.2Ų
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 1386.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)