Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
50.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.62, H-bond role recall 0.18
Reason: strain 50.4 kcal/mol
strain ΔE 50.4 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.911 kcal/mol/HA)
✓ Good fit quality (FQ -9.19)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Extreme strain energy (50.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-31.878
kcal/mol
LE
-0.911
kcal/mol/HA
Fit Quality
-9.19
FQ (Leeson)
HAC
35
heavy atoms
MW
480
Da
LogP
0.73
cLogP
Interaction summary
HB 9
HY 9
PI 1
CLASH 3
Interaction summary
HB 9
HY 9
PI 1
CLASH 3
| Final rank | 3.290 | Score | -31.878 |
|---|---|---|---|
| Inter norm | -0.884 | Intra norm | -0.027 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 9 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; high strain Δ 50.0 | ||
| Residues |
ALA158
ALA40
ALA48
ASN126
ASN41
ASP129
GLN42
GLY23
GLY47
LEU130
LEU31
LEU39
LYS127
LYS159
PHE38
SER157
SER27
SER28
| ||
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 | ||
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 | 15 | Native recall | 0.71 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 2 | Strict recall | 0.13 |
| HB same residue+role | 2 | HB role recall | 0.18 |
| HB same residue | 3 | HB residue recall | 0.27 |
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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 217 | 1.3512816325645542 | -0.920357 | -27.0109 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 327 | 2.562616059620716 | -0.697603 | -19.8611 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 264 | 2.6884770570826144 | -0.757765 | -24.6339 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 195 | 3.2904397737734246 | -0.883666 | -31.8781 | 9 | 18 | 15 | 0.71 | 0.18 | - | no | Current |
| 231 | 3.359211608723208 | -0.923712 | -28.1727 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 204 | 3.710670948551887 | -0.794939 | -28.899 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 236 | 3.7529471976223454 | -0.658299 | -21.2653 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 160 | 4.525021538507883 | -0.794752 | -29.6473 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 148 | 5.360865640556601 | -0.707003 | -22.203 | 10 | 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.
Scoring & efficiency
Docking score
-31.878kcal/mol
Ligand efficiency (LE)
-0.9108kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.187
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
480.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.73
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
50.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-6.58kcal/mol
Minimised FF energy
-56.97kcal/mol
SASA & burial
✓ computed
SASA (unbound)
753.0Ų
Total solvent-accessible surface area of free ligand
BSA total
609.4Ų
Buried surface area upon binding
BSA apolar
475.6Ų
Hydrophobic contacts buried
BSA polar
133.8Ų
Polar contacts buried
Fraction buried
80.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1438.3Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
515.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)