FAIRMol

Z44866976

Pose ID 9445 Compound 940 Pose 637

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 Z44866976
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
45.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.40, H-bond role recall 0.40
Burial
71%
Hydrophobic fit
74%
Reason: strain 45.5 kcal/mol
strain ΔE 45.5 kcal/mol 2 protein-contact clashes 70% of hydrophobic surface is solvent-exposed (14/20 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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.736 kcal/mol/HA) ✓ Good fit quality (FQ -7.17) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (71% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Extreme strain energy (45.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-22.826
kcal/mol
LE
-0.736
kcal/mol/HA
Fit Quality
-7.17
FQ (Leeson)
HAC
31
heavy atoms
MW
449
Da
LogP
0.91
cLogP
Strain ΔE
45.5 kcal/mol
SASA buried
71%
Lipo contact
74% BSA apolar/total
SASA unbound
694 Ų
Apolar buried
362 Ų

Interaction summary

HB 9 HY 1 PI 0 CLASH 2 ⚠ Exposure 70%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
70% of hydrophobic surface is solvent-exposed (14/20 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 20 Buried (contacted) 6 Exposed 14 LogP 0.91 H-bonds 9
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank3.276Score-22.826
Inter norm-0.871Intra norm0.135
Top1000noExcludedno
Contacts13H-bonds9
Artifact reasongeometry warning; 12 clashes; 1 protein clash; high strain Δ 45.1
Residues
ARG242 ARG337 ARG50 ASP243 ASP385 ASP47 GLU384 LEU339 PHE383 SER282 THR241 VAL335 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 overlap8Native recall0.53
Jaccard0.40RMSD-
HB strict1Strict recall0.17
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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
633 0.05829920103739172 -1.0551 -30.9043 6 13 0 0.00 0.00 - no Open
651 1.4156605545140337 -1.40297 -43.3583 15 18 0 0.00 0.00 - no Open
631 2.4700797108431822 -0.817046 -22.4274 2 16 0 0.00 0.00 - no Open
651 2.6241796803607684 -0.861067 -23.541 5 15 0 0.00 0.00 - no Open
641 2.867756166472061 -0.918058 -26.7937 7 12 0 0.00 0.00 - no Open
637 3.275743878737262 -0.87096 -22.8257 9 13 8 0.53 0.40 - no Current
650 3.2986306516203525 -1.05149 -29.1371 15 12 0 0.00 0.00 - no Open
628 4.031122152407257 -0.781668 -24.4719 5 16 0 0.00 0.00 - no Open
645 4.500872485938668 -0.819792 -23.1151 6 16 0 0.00 0.00 - no Open
651 4.7722691848813374 -1.01921 -26.299 12 18 0 0.00 0.00 - no Open
640 4.779003355861554 -1.06227 -31.24 16 18 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 -22.826kcal/mol
Ligand efficiency (LE) -0.7363kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.173
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 449.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.91
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 45.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 102.50kcal/mol
Minimised FF energy 57.05kcal/mol

SASA & burial

✓ computed
SASA (unbound) 693.5Ų
Total solvent-accessible surface area of free ligand
BSA total 492.3Ų
Buried surface area upon binding
BSA apolar 362.1Ų
Hydrophobic contacts buried
BSA polar 130.2Ų
Polar contacts buried
Fraction buried 71.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2465.3Ų
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 1368.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)