FAIRMol

Z19540043

Pose ID 9433 Compound 1450 Pose 625

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 Z19540043
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 mixed SASA done
Strain ΔE
23.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.32, H-bond role recall 0.20
Burial
78%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
1 protein-contact clashes 48% of hydrophobic surface appears solvent-exposed (15/31 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.453 kcal/mol/HA) ✓ Good fit quality (FQ -4.73) ✓ Good H-bonds (4 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ High strain energy (23.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (23)
Score
-18.121
kcal/mol
LE
-0.453
kcal/mol/HA
Fit Quality
-4.73
FQ (Leeson)
HAC
40
heavy atoms
MW
536
Da
LogP
4.73
cLogP
Strain ΔE
23.6 kcal/mol
SASA buried
78%
Lipo contact
79% BSA apolar/total
SASA unbound
837 Ų
Apolar buried
516 Ų

Interaction summary

HB 4 HY 22 PI 0 CLASH 1 ⚠ Exposure 48%
⚠️Partial hydrophobic solvent exposure
48% of hydrophobic surface appears solvent-exposed (15/31 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 31 Buried (contacted) 16 Exposed 15 LogP 4.73 H-bonds 4
Exposed fragments: phenyl (3/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank3.738Score-18.121
Inter norm-0.604Intra norm0.151
Top1000noExcludedno
Contacts18H-bonds4
Artifact reasongeometry warning; 23 clashes; 1 protein clash; moderate strain Δ 23.6
Residues
ARG22 ARG342 ASN20 CYS26 GLN341 GLU343 GLU384 LEU339 LEU350 LEU372 LEU382 PRO338 PRO340 PRO344 PRO373 THR21 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
Jaccard0.32RMSD-
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
624 3.6888057889596957 -0.617312 -26.825 3 17 0 0.00 0.00 - no Open
625 3.7378606056096007 -0.604217 -18.1212 4 18 8 0.53 0.20 - no Current
636 4.44380559423384 -0.718477 -29.0255 7 16 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 -18.121kcal/mol
Ligand efficiency (LE) -0.4530kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.731
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 40HA

Physicochemical properties
Molecular weight 535.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.73
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 67.72kcal/mol
Minimised FF energy 44.15kcal/mol

SASA & burial

✓ computed
SASA (unbound) 836.8Ų
Total solvent-accessible surface area of free ligand
BSA total 653.0Ų
Buried surface area upon binding
BSA apolar 516.4Ų
Hydrophobic contacts buried
BSA polar 136.5Ų
Polar contacts buried
Fraction buried 78.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2622.1Ų
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 1379.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)