FAIRMol

KB_HAT_25

Pose ID 3473 Compound 108 Pose 87

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
T06
T. brucei DHFR T. brucei
Ligand KB_HAT_25
PDB8RHT↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
23.1 kcal/mol
Protein clashes
11
Internal clashes
11
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.00
Burial
94%
Hydrophobic fit
78%
Reason: 1 severe internal clashes, 11 protein-contact clashes, 11 internal clashes
1 severe internal clashes 11 protein-contact clashes 11 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.656 kcal/mol/HA) ✓ Good fit quality (FQ -6.57) ✓ Good H-bonds (4 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ High strain energy (23.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-22.313
kcal/mol
LE
-0.656
kcal/mol/HA
Fit Quality
-6.57
FQ (Leeson)
HAC
34
heavy atoms
MW
476
Da
LogP
2.21
cLogP
Strain ΔE
23.1 kcal/mol
SASA buried
94%
Lipo contact
78% BSA apolar/total
SASA unbound
767 Ų
Apolar buried
560 Ų

Interaction summary

HB 4 HY 24 PI 4 CLASH 11 Severe 1
Final rank5.060Score-22.313
Inter norm-0.712Intra norm0.051
Top1000noExcludedno
Contacts21H-bonds4
Artifact reasongeometry warning; 16 clashes; 2 protein clashes; moderate strain Δ 21.0
Residues
ALA34 ARG100 ARG183 ARG59 ASP54 GLN56 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE58 PHE94 PRO91 THR184 TYR166 TYR57 VAL32 VAL33

Protein summary

223 residues
Protein targetT06Atoms3452
Residues223Chains1
Residue summaryARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

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:NDP301

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name8RHTContacts21
PoseOpen native poseHB0
IFP residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO91 SER89 THR184 THR86 TRP49 TYR166 TYR57 VAL32 VAL33
Current overlap17Native recall0.81
Jaccard0.68RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall0.25

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
116 0.9967124239667426 -0.835107 -24.9422 1 19 0 0.00 0.00 - no Open
145 1.3995751921199313 -0.88415 -27.5642 3 16 0 0.00 0.00 - no Open
182 1.4861130235883124 -0.855269 -26.7745 4 22 0 0.00 0.00 - no Open
140 1.615020829250697 -0.925503 -28.3157 6 17 1 0.05 0.00 - no Open
161 2.662027008092362 -0.751934 -23.4535 3 14 0 0.00 0.00 - no Open
149 3.0092960382301914 -0.757482 -21.0618 2 22 18 0.86 0.00 - no Open
117 3.133913752613804 -0.893126 -27.6382 10 20 0 0.00 0.00 - no Open
92 3.1897154297188073 -0.7343 -24.0617 7 15 0 0.00 0.00 - no Open
109 3.266242765469782 -0.81009 -22.6151 5 16 0 0.00 0.00 - no Open
95 3.6098926606982675 -0.795677 -23.8078 8 16 0 0.00 0.00 - no Open
150 3.6690791561020983 -0.768661 -24.4817 6 18 0 0.00 0.00 - no Open
91 3.8086261390469938 -0.740979 -20.0503 5 21 0 0.00 0.00 - no Open
124 4.692634237226219 -0.64544 -22.9491 7 15 0 0.00 0.00 - no Open
103 4.725842136853786 -0.76159 -22.4824 5 18 0 0.00 0.00 - no Open
118 4.790784883872673 -0.731769 -21.8142 8 17 0 0.00 0.00 - no Open
73 4.7962875837914805 -1.009 -30.2636 11 20 0 0.00 0.00 - no Open
46 5.044122438992116 -0.80531 -23.3978 7 15 0 0.00 0.00 - no Open
87 5.0598912182116695 -0.712441 -22.3133 4 21 17 0.81 0.00 - 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 -22.313kcal/mol
Ligand efficiency (LE) -0.6563kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.567
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 475.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.21
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 98.40kcal/mol
Minimised FF energy 75.26kcal/mol

SASA & burial

✓ computed
SASA (unbound) 767.1Ų
Total solvent-accessible surface area of free ligand
BSA total 721.0Ų
Buried surface area upon binding
BSA apolar 560.0Ų
Hydrophobic contacts buried
BSA polar 160.9Ų
Polar contacts buried
Fraction buried 94.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1837.7Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 572.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)