FAIRMol

Z56768366

Pose ID 8642 Compound 194 Pose 512

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
T13
T. brucei ODC (Active site) T. brucei Active site
Ligand Z56768366
PDB1F3T↗

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
12.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.63, Jaccard 0.52, H-bond role recall 0.29
Burial
78%
Hydrophobic fit
85%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.056 kcal/mol/HA) ✓ Good fit quality (FQ -10.08) ✓ Good H-bonds (5 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Moderate strain (12.0 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (13)
Score
-30.616
kcal/mol
LE
-1.056
kcal/mol/HA
Fit Quality
-10.08
FQ (Leeson)
HAC
29
heavy atoms
MW
426
Da
LogP
5.37
cLogP
Strain ΔE
12.0 kcal/mol
SASA buried
78%
Lipo contact
85% BSA apolar/total
SASA unbound
661 Ų
Apolar buried
440 Ų

Interaction summary

HB 5 HY 16 PI 4 CLASH 2
Final rank2.493Score-30.616
Inter norm-1.100Intra norm0.045
Top1000noExcludedno
Contacts16H-bonds5
Artifact reasongeometry warning; 13 clashes; 1 protein clash
Residues
ALA67 ARG277 ASN327 ASP332 CYS328 GLU274 GLY199 GLY236 GLY237 GLY276 GLY393 HIS197 LYS69 SER200 TYR331 TYR389

Protein summary

411 residues
Protein targetT13Atoms6340
Residues411Chains1
Residue summaryVAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1F3TContacts19
PoseOpen native poseHB0
IFP residues
ALA111 ALA67 ARG154 ARG277 ASP332 ASP88 CYS70 GLU274 GLY236 GLY237 GLY276 HIS197 LYS69 PHE238 PRO275 SER200 TYR278 TYR331 TYR389
Current overlap12Native recall0.63
Jaccard0.52RMSD-
HB strict1Strict recall0.11
HB same residue+role2HB role recall0.29
HB same residue3HB residue recall0.43

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
487 1.088329866091016 -1.17165 -32.6657 5 19 0 0.00 0.00 - no Open
511 1.2374971441566485 -1.20348 -26.4937 4 18 0 0.00 0.00 - no Open
548 1.4904529892984921 -0.920653 -22.5653 9 17 0 0.00 0.00 - no Open
521 1.81825799653337 -0.897538 -26.5745 4 17 0 0.00 0.00 - no Open
565 2.2544588790717133 -0.826268 -25.3055 8 11 0 0.00 0.00 - no Open
530 2.3192700841994296 -0.96341 -25.2468 1 20 0 0.00 0.00 - no Open
512 2.4932728018700403 -1.10026 -30.6157 5 16 12 0.63 0.29 - no Current
541 2.508845732894417 -0.876449 -24.5843 1 18 0 0.00 0.00 - no Open
522 2.531497306555514 -0.838818 -22.236 1 15 0 0.00 0.00 - no Open
543 2.556193085876479 -0.766219 -16.5141 5 18 0 0.00 0.00 - no Open
503 2.6989153506438197 -0.909917 -24.0506 6 16 0 0.00 0.00 - no Open
508 3.0900948345735757 -0.897584 -21.3907 7 15 0 0.00 0.00 - no Open
516 3.307089045836197 -0.707354 -18.8371 3 12 0 0.00 0.00 - no Open
499 3.642356120158013 -1.12423 -30.5543 8 18 0 0.00 0.00 - no Open
511 3.6596004503079134 -0.851044 -25.8511 6 13 0 0.00 0.00 - no Open
504 4.110164392350293 -1.09071 -27.3774 9 16 0 0.00 0.00 - no Open
550 4.159361593789174 -0.833109 -22.8091 6 11 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 -30.616kcal/mol
Ligand efficiency (LE) -1.0557kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.078
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 425.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.37
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 25.64kcal/mol
Minimised FF energy 13.60kcal/mol

SASA & burial

✓ computed
SASA (unbound) 660.7Ų
Total solvent-accessible surface area of free ligand
BSA total 518.9Ų
Buried surface area upon binding
BSA apolar 440.3Ų
Hydrophobic contacts buried
BSA polar 78.6Ų
Polar contacts buried
Fraction buried 78.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2634.3Ų
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 3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1377.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)