Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
24.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.67, Jaccard 0.54, H-bond role recall 0.18
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
55% of hydrophobic surface appears solvent-exposed (12/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.901 kcal/mol/HA)
✓ Good fit quality (FQ -8.50)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (24.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-25.221
kcal/mol
LE
-0.901
kcal/mol/HA
Fit Quality
-8.50
FQ (Leeson)
HAC
28
heavy atoms
MW
383
Da
LogP
4.18
cLogP
Interaction summary
HB 11
HY 4
PI 1
CLASH 4
⚠ Exposure 54%
Interaction summary
HB 11
HY 4
PI 1
CLASH 4
⚠ Exposure 54%
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
Partial hydrophobic solvent exposure
55% of hydrophobic surface appears solvent-exposed (12/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22
Buried (contacted) 10
Exposed 12
LogP 4.18
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 3.726 | Score | -25.221 |
|---|---|---|---|
| Inter norm | -1.119 | Intra norm | 0.218 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 11 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; moderate strain Δ 24.3 | ||
| Residues |
ALA158
ALA24
ALA70
ASN126
ASN41
ASP68
GLU73
GLY23
GLY25
GLY71
LEU130
LYS127
LYS159
LYS26
PHE38
SER27
SER28
THR44
THR69
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 14 | Native recall | 0.67 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 2 | Strict recall | 0.13 |
| HB same residue+role | 2 | HB role recall | 0.18 |
| HB same residue | 4 | HB residue recall | 0.36 |
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 219 | 3.7256128415218974 | -1.11878 | -25.221 | 11 | 19 | 14 | 0.67 | 0.18 | - | no | Current |
| 198 | 3.9842481232822697 | -0.973209 | -21.3791 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 237 | 4.294682454974666 | -0.940131 | -23.3757 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 275 | 4.305069637199369 | -0.859397 | -23.1393 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 257 | 4.592849993278926 | -1.02176 | -20.928 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 296 | 5.005811361214491 | -0.717319 | -18.4462 | 8 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 181 | 5.423532920502459 | -1.10466 | -23.9334 | 14 | 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.
Scoring & efficiency
Docking score
-25.221kcal/mol
Ligand efficiency (LE)
-0.9008kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.503
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
383.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.18
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
55.88kcal/mol
Minimised FF energy
31.60kcal/mol
SASA & burial
✓ computed
SASA (unbound)
669.2Ų
Total solvent-accessible surface area of free ligand
BSA total
553.8Ų
Buried surface area upon binding
BSA apolar
450.3Ų
Hydrophobic contacts buried
BSA polar
103.5Ų
Polar contacts buried
Fraction buried
82.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1422.8Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
509.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)