FAIRMol

Z56773052

Pose ID 9213 Compound 3179 Pose 405

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 Z56773052
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
13.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.44, H-bond role recall 0.20
Burial
73%
Hydrophobic fit
86%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 71% of hydrophobic surface is solvent-exposed (15/21 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 ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.759 kcal/mol/HA) ✓ Good fit quality (FQ -7.16) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ Moderate strain (13.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-21.243
kcal/mol
LE
-0.759
kcal/mol/HA
Fit Quality
-7.16
FQ (Leeson)
HAC
28
heavy atoms
MW
406
Da
LogP
5.56
cLogP
Strain ΔE
13.3 kcal/mol
SASA buried
73%
Lipo contact
86% BSA apolar/total
SASA unbound
659 Ų
Apolar buried
413 Ų

Interaction summary

HB 6 HY 2 PI 0 CLASH 3 ⚠ Exposure 71%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
71% of hydrophobic surface is solvent-exposed (15/21 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 21 Buried (contacted) 6 Exposed 15 LogP 5.56 H-bonds 6
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)phenyl (1/5 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank2.391Score-21.243
Inter norm-0.781Intra norm0.022
Top1000noExcludedno
Contacts11H-bonds6
Artifact reasongeometry warning; 9 clashes; 1 protein clash
Residues
ARG242 ARG337 ASP243 ASP385 ASP47 GLU384 GLY240 LEU339 LYS51 SER282 THR241

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 overlap8Native recall0.53
Jaccard0.44RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
408 0.6856936610759928 -0.912214 -16.18 4 20 0 0.00 0.00 - no Open
385 1.7574554438791103 -0.85316 -21.8276 3 16 0 0.00 0.00 - no Open
405 2.3914850059656008 -0.780922 -21.2429 6 11 8 0.53 0.20 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -21.243kcal/mol
Ligand efficiency (LE) -0.7587kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.162
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 405.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.56
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 13.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 68.48kcal/mol
Minimised FF energy 55.13kcal/mol

SASA & burial

✓ computed
SASA (unbound) 659.0Ų
Total solvent-accessible surface area of free ligand
BSA total 479.4Ų
Buried surface area upon binding
BSA apolar 412.6Ų
Hydrophobic contacts buried
BSA polar 66.8Ų
Polar contacts buried
Fraction buried 72.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2445.9Ų
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 1403.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)