FAIRMol

Z54322503

Pose ID 9333 Compound 3726 Pose 525

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 Z54322503
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
54.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.30, H-bond role recall 0.20
Burial
83%
Hydrophobic fit
84%
Reason: strain 54.5 kcal/mol
strain ΔE 54.5 kcal/mol 1 protein-contact clashes 59% of hydrophobic surface appears solvent-exposed (16/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.554 kcal/mol/HA) ✓ Good fit quality (FQ -5.59) ✓ Good H-bonds (3 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Extreme strain energy (54.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-19.407
kcal/mol
LE
-0.554
kcal/mol/HA
Fit Quality
-5.59
FQ (Leeson)
HAC
35
heavy atoms
MW
463
Da
LogP
5.73
cLogP
Strain ΔE
54.5 kcal/mol
SASA buried
83%
Lipo contact
84% BSA apolar/total
SASA unbound
801 Ų
Apolar buried
558 Ų

Interaction summary

HB 3 HY 8 PI 0 CLASH 1 ⚠ Exposure 59%
⚠️Partial hydrophobic solvent exposure
59% of hydrophobic surface appears solvent-exposed (16/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 27 Buried (contacted) 11 Exposed 16 LogP 5.73 H-bonds 3
Exposed fragments: phenyl (3/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank2.571Score-19.407
Inter norm-0.656Intra norm0.102
Top1000noExcludedno
Contacts20H-bonds3
Artifact reasongeometry warning; 13 clashes; 1 protein clash; high strain Δ 54.5
Residues
ARG22 ARG342 ASN20 ASP44 CYS26 GLN341 GLU343 LEU25 LEU339 LEU350 LEU372 LEU382 PRO338 PRO340 PRO344 PRO373 THR21 THR285 TYR370 TYR371

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
Jaccard0.30RMSD-
HB strict1Strict recall0.17
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
537 2.3056810698099706 -0.585945 -21.4545 5 13 0 0.00 0.00 - no Open
525 2.5708965602452896 -0.656142 -19.4069 3 20 8 0.53 0.20 - no Current
546 2.7435894818912305 -0.682717 -17.6049 5 13 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 -19.407kcal/mol
Ligand efficiency (LE) -0.5545kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.593
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 463.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.73
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 54.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 178.56kcal/mol
Minimised FF energy 124.09kcal/mol

SASA & burial

✓ computed
SASA (unbound) 801.4Ų
Total solvent-accessible surface area of free ligand
BSA total 666.5Ų
Buried surface area upon binding
BSA apolar 558.2Ų
Hydrophobic contacts buried
BSA polar 108.3Ų
Polar contacts buried
Fraction buried 83.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2608.0Ų
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 1395.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)